Variant rs2281575 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001174089.2(SLC4A11):c.2193-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 1,611,638 control chromosomes in the GnomAD database, including 159,860 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 13246 hom., cov: 32)

Exomes 𝑓: 0.44 ( 146614 hom. )

Consequence

SLC4A11
NM_001174089.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.726

Variant links:

Genes affected

SLC4A11 (HGNC:16438): (solute carrier family 4 member 11) This gene encodes a voltage-regulated, electrogenic sodium-coupled borate cotransporter that is essential for borate homeostasis, cell growth and cell proliferation. Mutations in this gene have been associated with a number of endothelial corneal dystrophies including recessive corneal endothelial dystrophy 2, corneal dystrophy and perceptive deafness, and Fuchs endothelial corneal dystrophy. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Mar 2010]

SLC4A11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 20-3228725-G-A is Benign according to our data. Variant chr20-3228725-G-A is described in ClinVar as [Benign]. Clinvar id is 261998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-3228725-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC4A11	NM_001174089.2 linkuse as main transcript	c.2193-18C>T		intron_variant		ENST00000642402.1	NP_001167560.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC4A11	ENST00000642402.1 linkuse as main transcript	c.2193-18C>T		intron_variant			NM_001174089.2	ENSP00000493503	P2	Q8NBS3-3

Frequencies

GnomAD3 genomes

AF:

0.409

AC:

62135

AN:

151924

Hom.:

13239

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.372

Gnomad ASJ

AF:

0.435

Gnomad EAS

AF:

0.700

Gnomad SAS

AF:

0.553

Gnomad FIN

AF:

0.362

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.427

GnomAD3 exomes

AF:

0.443

AC:

109002

AN:

245870

Hom.:

25272

AF XY:

0.451

AC XY:

60272

AN XY:

133558

show subpopulations

Gnomad AFR exome

AF:

0.330

Gnomad AMR exome

AF:

0.348

Gnomad ASJ exome

AF:

0.435

Gnomad EAS exome

AF:

0.698

Gnomad SAS exome

AF:

0.548

Gnomad FIN exome

AF:

0.370

Gnomad NFE exome

AF:

0.433

Gnomad OTH exome

AF:

0.440

GnomAD4 exome

AF:

0.444

AC:

647438

AN:

1459596

Hom.:

146614

Cov.:

AF XY:

0.446

AC XY:

323932

AN XY:

726050

show subpopulations

Gnomad4 AFR exome

AF:

0.328

Gnomad4 AMR exome

AF:

0.351

Gnomad4 ASJ exome

AF:

0.438

Gnomad4 EAS exome

AF:

0.708

Gnomad4 SAS exome

AF:

0.538

Gnomad4 FIN exome

AF:

0.374

Gnomad4 NFE exome

AF:

0.437

Gnomad4 OTH exome

AF:

0.452

GnomAD4 genome

AF:

0.409

AC:

62160

AN:

152042

Hom.:

13246

Cov.:

AF XY:

0.408

AC XY:

30362

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.329

Gnomad4 AMR

AF:

0.372

Gnomad4 ASJ

AF:

0.435

Gnomad4 EAS

AF:

0.699

Gnomad4 SAS

AF:

0.554

Gnomad4 FIN

AF:

0.362

Gnomad4 NFE

AF:

0.437

Gnomad4 OTH

AF:

0.430

Alfa

AF:

0.420

Hom.:

3827

Bravo

AF:

0.402

Asia WGS

AF:

0.638

AC:

2217

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Corneal dystrophy-perceptive deafness syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Congenital hereditary endothelial dystrophy of cornea

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.093

DANN

Benign

0.84

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

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