Genetic Variant SLC4A2:c.1147+95G>C (chr7-151068149-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_003040.4(SLC4A2):c.1147+95G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SLC4A2
NM_003040.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395

Publications

5 publications found

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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC4A2	NM_003040.4 link	c.1147+95G>C	intron_variant	Intron 8 of 22	ENST00000413384.7	NP_003031.3	P04920-1
SLC4A2	NM_001199692.3 link	c.1147+95G>C	intron_variant	Intron 8 of 22		NP_001186621.1	P04920-1Q59GF1
SLC4A2	NM_001199693.1 link	c.1120+95G>C	intron_variant	Intron 7 of 21		NP_001186622.1	P04920-3Q59GF1
SLC4A2	NM_001199694.2 link	c.1105+95G>C	intron_variant	Intron 7 of 21		NP_001186623.1	P04920-2Q59GF1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC4A2	ENST00000413384.7 link	c.1147+95G>C		intron_variant	Intron 8 of 22	1	NM_003040.4	ENSP00000405600.2		P04920-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

810610

Hom.:

AF XY:

0.00

AC XY:

AN XY:

400536

African (AFR)

AF:

0.00

AC:

AN:

16666

American (AMR)

AF:

0.00

AC:

AN:

9984

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14962

East Asian (EAS)

AF:

0.00

AC:

AN:

26438

South Asian (SAS)

AF:

0.00

AC:

AN:

40628

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31004

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2972

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

630642

Other (OTH)

AF:

0.00

AC:

AN:

37314

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

3178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.68

(source)

DANN

Benign

0.63

PhyloP100

-0.40

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over