Variant 7-151071699-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003040.4(SLC4A2):c.2202G>A(p.Thr734=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,608,334 control chromosomes in the GnomAD database, including 168,097 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 14512 hom., cov: 31)

Exomes 𝑓: 0.46 ( 153585 hom. )

Consequence

SLC4A2
NM_003040.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.15

Variant links:

Genes affected

SLC4A2 (HGNC:11028): (solute carrier family 4 member 2) This gene encodes a member of the anion exchanger family of membrane transport proteins. The encoded protein regulates intracellular pH, biliary bicarbonate secretion, and chloride uptake. Reduced expression of this gene may be associated with primary biliary cirrhosis (PBC) in human patients, while differential expression of this gene may be associated with malignant hepatocellular carcinoma, colon and gastric cancers. [provided by RefSeq, Nov 2016]

SLC4A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP7

Synonymous conserved (PhyloP=-5.15 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SLC4A2	NM_003040.4 linkuse as main transcript	c.2202G>A	p.Thr734=	synonymous_variant	15/23	ENST00000413384.7	NP_003031.3
SLC4A2	NM_001199692.3 linkuse as main transcript	c.2202G>A	p.Thr734=	synonymous_variant	15/23		NP_001186621.1
SLC4A2	NM_001199693.1 linkuse as main transcript	c.2175G>A	p.Thr725=	synonymous_variant	14/22		NP_001186622.1
SLC4A2	NM_001199694.2 linkuse as main transcript	c.2160G>A	p.Thr720=	synonymous_variant	14/22		NP_001186623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC4A2	ENST00000413384.7 linkuse as main transcript	c.2202G>A	p.Thr734=	synonymous_variant	15/23	1	NM_003040.4	ENSP00000405600	P1	P04920-1

Frequencies

GnomAD3 genomes

AF:

0.433

AC:

65629

AN:

151732

Hom.:

14505

Cov.:

show subpopulations

Gnomad AFR

AF:

0.362

Gnomad AMI

AF:

0.542

Gnomad AMR

AF:

0.522

Gnomad ASJ

AF:

0.478

Gnomad EAS

AF:

0.428

Gnomad SAS

AF:

0.536

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.446

Gnomad OTH

AF:

0.433

GnomAD3 exomes

AF:

0.482

AC:

119610

AN:

247944

Hom.:

29959

AF XY:

0.480

AC XY:

64293

AN XY:

134046

show subpopulations

Gnomad AFR exome

AF:

0.361

Gnomad AMR exome

AF:

0.660

Gnomad ASJ exome

AF:

0.467

Gnomad EAS exome

AF:

0.433

Gnomad SAS exome

AF:

0.540

Gnomad FIN exome

AF:

0.424

Gnomad NFE exome

AF:

0.451

Gnomad OTH exome

AF:

0.477

GnomAD4 exome

AF:

0.456

AC:

664643

AN:

1456486

Hom.:

153585

Cov.:

AF XY:

0.458

AC XY:

331791

AN XY:

724030

show subpopulations

Gnomad4 AFR exome

AF:

0.362

Gnomad4 AMR exome

AF:

0.650

Gnomad4 ASJ exome

AF:

0.466

Gnomad4 EAS exome

AF:

0.428

Gnomad4 SAS exome

AF:

0.540

Gnomad4 FIN exome

AF:

0.427

Gnomad4 NFE exome

AF:

0.447

Gnomad4 OTH exome

AF:

0.454

GnomAD4 genome

AF:

0.432

AC:

65661

AN:

151848

Hom.:

14512

Cov.:

AF XY:

0.435

AC XY:

32261

AN XY:

74190

show subpopulations

Gnomad4 AFR

AF:

0.362

Gnomad4 AMR

AF:

0.523

Gnomad4 ASJ

AF:

0.478

Gnomad4 EAS

AF:

0.428

Gnomad4 SAS

AF:

0.533

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.446

Gnomad4 OTH

AF:

0.438

Alfa

AF:

0.430

Hom.:

17843

Bravo

AF:

0.440

Asia WGS

AF:

0.494

AC:

1717

AN:

3478

EpiCase

AF:

0.436

EpiControl

AF:

0.437

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

2.5

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over