rs5017

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_000342.4(SLC4A1):c.1323G>A(p.Leu441=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 1,613,902 control chromosomes in the GnomAD database, including 4,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.051 ( 286 hom., cov: 31)

Exomes 𝑓: 0.070 ( 4066 hom. )

Consequence

SLC4A1
NM_000342.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 0.346

Variant links:

Genes affected

SLC4A1 (HGNC:11027): (solute carrier family 4 member 1 (Diego blood group)) The protein encoded by this gene is part of the anion exchanger (AE) family and is expressed in the erythrocyte plasma membrane, where it functions as a chloride/bicarbonate exchanger involved in carbon dioxide transport from tissues to lungs. The protein comprises two domains that are structurally and functionally distinct. The N-terminal 40kDa domain is located in the cytoplasm and acts as an attachment site for the red cell skeleton by binding ankyrin. The glycosylated C-terminal membrane-associated domain contains 12-14 membrane spanning segments and carries out the stilbene disulphonate-sensitive exchange transport of anions. The cytoplasmic tail at the extreme C-terminus of the membrane domain binds carbonic anhydrase II. The encoded protein associates with the red cell membrane protein glycophorin A and this association promotes the correct folding and translocation of the exchanger. This protein is predominantly dimeric but forms tetramers in the presence of ankyrin. Many mutations in this gene are known in man, and these mutations can lead to two types of disease: destabilization of red cell membrane leading to hereditary spherocytosis, and defective kidney acid secretion leading to distal renal tubular acidosis. Other mutations that do not give rise to disease result in novel blood group antigens, which form the Diego blood group system. Southeast Asian ovalocytosis (SAO, Melanesian ovalocytosis) results from the heterozygous presence of a deletion in the encoded protein and is common in areas where Plasmodium falciparum malaria is endemic. One null mutation in this gene is known, resulting in very severe anemia and nephrocalcinosis. [provided by RefSeq, Jul 2008]

SLC4A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 17-44257767-C-T is Benign according to our data. Variant chr17-44257767-C-T is described in ClinVar as [Benign]. Clinvar id is 255905.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-44257767-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.346 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SLC4A1	NM_000342.4 linkuse as main transcript	c.1323G>A	p.Leu441=	synonymous_variant	12/20	ENST00000262418.12
SLC4A1	XM_011525129.3 linkuse as main transcript	c.1323G>A	p.Leu441=	synonymous_variant	12/19
SLC4A1	XM_005257593.6 linkuse as main transcript	c.1128G>A	p.Leu376=	synonymous_variant	10/18
SLC4A1	XM_011525130.2 linkuse as main transcript	c.1323G>A	p.Leu441=	synonymous_variant	12/18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC4A1	ENST00000262418.12 linkuse as main transcript	c.1323G>A	p.Leu441=	synonymous_variant	12/20	1	NM_000342.4	P1	P02730-1
SLC4A1	ENST00000399246.3 linkuse as main transcript	c.777+1495G>A		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0509

AC:

7748

AN:

152128

Hom.:

286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0137

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.0395

Gnomad ASJ

AF:

0.0920

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0137

Gnomad FIN

AF:

0.0410

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0817

Gnomad OTH

AF:

0.0550

GnomAD3 exomes

AF:

0.0523

AC:

13103

AN:

250552

Hom.:

465

AF XY:

0.0532

AC XY:

7200

AN XY:

135444

show subpopulations

Gnomad AFR exome

AF:

0.0139

Gnomad AMR exome

AF:

0.0291

Gnomad ASJ exome

AF:

0.0966

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0179

Gnomad FIN exome

AF:

0.0405

Gnomad NFE exome

AF:

0.0805

Gnomad OTH exome

AF:

0.0622

GnomAD4 exome

AF:

0.0698

AC:

101991

AN:

1461656

Hom.:

4066

Cov.:

AF XY:

0.0690

AC XY:

50161

AN XY:

727126

show subpopulations

Gnomad4 AFR exome

AF:

0.0120

Gnomad4 AMR exome

AF:

0.0310

Gnomad4 ASJ exome

AF:

0.0962

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.0197

Gnomad4 FIN exome

AF:

0.0444

Gnomad4 NFE exome

AF:

0.0805

Gnomad4 OTH exome

AF:

0.0617

GnomAD4 genome

AF:

0.0509

AC:

7743

AN:

152246

Hom.:

286

Cov.:

AF XY:

0.0477

AC XY:

3553

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.0137

Gnomad4 AMR

AF:

0.0393

Gnomad4 ASJ

AF:

0.0920

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0135

Gnomad4 FIN

AF:

0.0410

Gnomad4 NFE

AF:

0.0817

Gnomad4 OTH

AF:

0.0540

Alfa

AF:

0.0756

Hom.:

592

Bravo

AF:

0.0489

Asia WGS

AF:

0.00982

AC:

AN:

3478

EpiCase

AF:

0.0856

EpiControl

AF:

0.0848

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 09, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 22, 2019	- -

Autosomal dominant distal renal tubular acidosis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Hereditary spherocytosis type 4

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

Hemolytic anemia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

Cadd

Benign

5.2

Dann

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over