Variant 2-161965134-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001178015.2(SLC4A10):c.3120C>T(p.Pro1040Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,609,384 control chromosomes in the GnomAD database, including 363 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.013 ( 41 hom., cov: 32)

Exomes 𝑓: 0.015 ( 322 hom. )

Consequence

SLC4A10
NM_001178015.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.611

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BP6

Variant 2-161965134-C-T is Benign according to our data. Variant chr2-161965134-C-T is described in ClinVar as [Benign]. Clinvar id is 586610.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.611 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0924 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.3120C>T	p.Pro1040Pro	synonymous_variant	23/27	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.3120C>T	p.Pro1040Pro	synonymous_variant	23/27	1	NM_001178015.2	ENSP00000393066.1		Q6U841-1

Frequencies

GnomAD3 genomes

AF:

0.0133

AC:

2011

AN:

151086

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00363

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0151

Gnomad ASJ

AF:

0.00952

Gnomad EAS

AF:

0.0998

Gnomad SAS

AF:

0.0307

Gnomad FIN

AF:

0.00337

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0129

Gnomad OTH

AF:

0.0101

GnomAD3 exomes

AF:

0.0192

AC:

4761

AN:

247378

Hom.:

113

AF XY:

0.0193

AC XY:

2594

AN XY:

134270

show subpopulations

Gnomad AFR exome

AF:

0.00423

Gnomad AMR exome

AF:

0.0172

Gnomad ASJ exome

AF:

0.00848

Gnomad EAS exome

AF:

0.0948

Gnomad SAS exome

AF:

0.0267

Gnomad FIN exome

AF:

0.00419

Gnomad NFE exome

AF:

0.0119

Gnomad OTH exome

AF:

0.0163

GnomAD4 exome

AF:

0.0151

AC:

22042

AN:

1458182

Hom.:

322

Cov.:

AF XY:

0.0155

AC XY:

11220

AN XY:

725354

show subpopulations

Gnomad4 AFR exome

AF:

0.00362

Gnomad4 AMR exome

AF:

0.0166

Gnomad4 ASJ exome

AF:

0.00746

Gnomad4 EAS exome

AF:

0.0828

Gnomad4 SAS exome

AF:

0.0261

Gnomad4 FIN exome

AF:

0.00451

Gnomad4 NFE exome

AF:

0.0127

Gnomad4 OTH exome

AF:

0.0178

GnomAD4 genome

AF:

0.0133

AC:

2014

AN:

151202

Hom.:

Cov.:

AF XY:

0.0140

AC XY:

1035

AN XY:

73838

show subpopulations

Gnomad4 AFR

AF:

0.00362

Gnomad4 AMR

AF:

0.0151

Gnomad4 ASJ

AF:

0.00952

Gnomad4 EAS

AF:

0.0995

Gnomad4 SAS

AF:

0.0310

Gnomad4 FIN

AF:

0.00337

Gnomad4 NFE

AF:

0.0129

Gnomad4 OTH

AF:

0.0119

Alfa

AF:

0.00956

Hom.:

Bravo

AF:

0.0132

Asia WGS

AF:

0.0650

AC:

224

AN:

3478

EpiCase

AF:

0.0121

EpiControl

AF:

0.0118

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	Aug 15, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

5.1

DANN

Benign

0.63

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