rs2857078

Variant names:

• chr17-44252803-A-C
• rs2857078
• NM_000342.4:c.2311+315T>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000342.4(SLC4A1):​c.2311+315T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,098 control chromosomes in the GnomAD database, including 29,995 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.62 (29995 hom., cov: 32)
• Consequence: SLC4A1 NM_000342.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.230
• Publications: 15 publications found

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 Gene-Disease associations (from GenCC):

• autosomal dominant distal renal tubular acidosis

  Inheritance: AD, AR Classification: STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)
• hereditary spherocytosis type 4

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• renal tubular acidosis, distal, 4, with hemolytic anemia

  Inheritance: AD, AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• southeast Asian ovalocytosis

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
• dehydrated hereditary stomatocytosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary spherocytosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• cryohydrocytosis

  Inheritance: Unknown, AD Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 17-44252803-A-C is Benign according to our data. Variant chr17-44252803-A-C is described in ClinVar as [Benign]. Clinvar id is 1181739.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC4A1	NM_000342.4	c.2311+315T>G		intron_variant	Intron 17 of 19	ENST00000262418.12	NP_000333.1
SLC4A1	XM_011525129.3	c.2221+315T>G		intron_variant	Intron 16 of 18		XP_011523431.1
SLC4A1	XM_005257593.6	c.2116+315T>G		intron_variant	Intron 15 of 17		XP_005257650.1
SLC4A1	XM_011525130.2	c.2311+315T>G		intron_variant	Intron 17 of 17		XP_011523432.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC4A1	ENST00000262418.12	c.2311+315T>G		intron_variant	Intron 17 of 19	1	NM_000342.4	ENSP00000262418.6
SLC4A1	ENST00000399246.3	c.1213+315T>G		intron_variant	Intron 12 of 14	5		ENSP00000382190.3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93655 AN: 151980 Hom.: 29977 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.625

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.616 AC: 93721 AN: 152098 Hom.: 29995 Cov.: 32 AF XY: 0.618 AC XY: 45927 AN XY: 74340

African (AFR) AF: 0.502 AC: 20799 AN: 41440

American (AMR) AF: 0.603 AC: 9220 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1902 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1218 AN: 5168

South Asian (SAS) AF: 0.693 AC: 3343 AN: 4824

European-Finnish (FIN) AF: 0.758 AC: 8032 AN: 10594

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46958 AN: 67998

Other (OTH) AF: 0.624 AC: 1320 AN: 2114

Alfa AF: 0.652 Hom.: 6651

Bravo AF: 0.597

Asia WGS AF: 0.484 AC: 1684 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 20, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.25
DANN	Benign	0.54
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2857078; hg19: chr17-42330171;