Variant chr2-161839904-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001354455.2(SLC4A10):c.-293C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0713 in 1,613,532 control chromosomes in the GnomAD database, including 4,603 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.061 ( 368 hom., cov: 32)

Exomes 𝑓: 0.072 ( 4235 hom. )

Consequence

SLC4A10
NM_001354455.2 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.322

Variant links:

Genes affected

SLC4A10 (HGNC:13811): (solute carrier family 4 member 10) This gene belongs to a small family of sodium-coupled bicarbonate transporters (NCBTs) that regulate the intracellular pH of neurons, the secretion of bicarbonate ions across the choroid plexus, and the pH of the brain extracellular fluid. The protein encoded by this gene was initially identified as a sodium-driven chloride bicarbonate exchanger (NCBE) though there is now evidence that its sodium/bicarbonate cotransport activity is independent of any chloride ion countertransport under physiological conditions. This gene is now classified as a member A10 of the SLC4 family of transmembrane solute carriers. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010]

SLC4A10 links:

SLC4A10 (HGNC:):

SLC4A10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP6

Variant 2-161839904-C-T is Benign according to our data. Variant chr2-161839904-C-T is described in ClinVar as [Benign]. Clinvar id is 586611.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC4A10	NM_001178015.2 linkuse as main transcript	c.393C>T	p.Asp131Asp	synonymous_variant	4/27	ENST00000446997.6	NP_001171486.1	Q6U841-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC4A10	ENST00000446997.6 linkuse as main transcript	c.393C>T	p.Asp131Asp	synonymous_variant	4/27	1	NM_001178015.2	ENSP00000393066.1		Q6U841-1

Frequencies

GnomAD3 genomes

AF:

0.0607

AC:

9230

AN:

151984

Hom.:

367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0136

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.0652

Gnomad ASJ

AF:

0.0331

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.0861

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0729

Gnomad OTH

AF:

0.0699

GnomAD3 exomes

AF:

0.0736

AC:

18345

AN:

249270

Hom.:

831

AF XY:

0.0758

AC XY:

10252

AN XY:

135228

show subpopulations

Gnomad AFR exome

AF:

0.0118

Gnomad AMR exome

AF:

0.0471

Gnomad ASJ exome

AF:

0.0346

Gnomad EAS exome

AF:

0.128

Gnomad SAS exome

AF:

0.0790

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.0755

Gnomad OTH exome

AF:

0.0762

GnomAD4 exome

AF:

0.0724

AC:

105851

AN:

1461430

Hom.:

4235

Cov.:

AF XY:

0.0735

AC XY:

53468

AN XY:

727010

show subpopulations

Gnomad4 AFR exome

AF:

0.0109

Gnomad4 AMR exome

AF:

0.0482

Gnomad4 ASJ exome

AF:

0.0340

Gnomad4 EAS exome

AF:

0.121

Gnomad4 SAS exome

AF:

0.0790

Gnomad4 FIN exome

AF:

0.112

Gnomad4 NFE exome

AF:

0.0725

Gnomad4 OTH exome

AF:

0.0666

GnomAD4 genome

AF:

0.0607

AC:

9234

AN:

152102

Hom.:

368

Cov.:

AF XY:

0.0637

AC XY:

4735

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0135

Gnomad4 AMR

AF:

0.0652

Gnomad4 ASJ

AF:

0.0331

Gnomad4 EAS

AF:

0.133

Gnomad4 SAS

AF:

0.0868

Gnomad4 FIN

AF:

0.117

Gnomad4 NFE

AF:

0.0729

Gnomad4 OTH

AF:

0.0716

Alfa

AF:

0.0700

Hom.:

664

Bravo

AF:

0.0550

Asia WGS

AF:

0.101

AC:

352

AN:

3478

EpiCase

AF:

0.0747

EpiControl

AF:

0.0786

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	May 07, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.27

CADD

Benign

DANN

Benign

0.58

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.20

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.20

Position offset: -8

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