rs13247141

Variant names:

• chr7-151068385-C-T
• rs13247141
• NM_003040.4:c.1147+331C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003040.4(SLC4A2):​c.1147+331C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 151,920 control chromosomes in the GnomAD database, including 3,993 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 0.21 (3993 hom., cov: 32)
• Consequence: SLC4A2 NM_003040.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC4A2	NM_003040.4	c.1147+331C>T		intron_variant	Intron 8 of 22	ENST00000413384.7	NP_003031.3
SLC4A2	NM_001199692.3	c.1147+331C>T		intron_variant	Intron 8 of 22		NP_001186621.1
SLC4A2	NM_001199693.1	c.1120+331C>T		intron_variant	Intron 7 of 21		NP_001186622.1
SLC4A2	NM_001199694.2	c.1105+331C>T		intron_variant	Intron 7 of 21		NP_001186623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC4A2	ENST00000413384.7	c.1147+331C>T		intron_variant	Intron 8 of 22	1	NM_003040.4	ENSP00000405600.2

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32575 AN: 151802 Hom.: 3980 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.219

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.215 AC: 32597 AN: 151920 Hom.: 3993 Cov.: 32 AF XY: 0.223 AC XY: 16581 AN XY: 74242

African (AFR) AF: 0.142 AC: 5899 AN: 41424

American (AMR) AF: 0.371 AC: 5668 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 907 AN: 3470

East Asian (EAS) AF: 0.313 AC: 1615 AN: 5156

South Asian (SAS) AF: 0.241 AC: 1155 AN: 4800

European-Finnish (FIN) AF: 0.265 AC: 2796 AN: 10554

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13650 AN: 67928

Other (OTH) AF: 0.219 AC: 462 AN: 2110

Alfa AF: 0.210 Hom.: 717

Bravo AF: 0.225

Asia WGS AF: 0.294 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.67
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13247141; hg19: chr7-150765472;