7-151075830-C-T

Position:

• chr7-151075830-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003040.4(SLC4A2):​c.3471+55C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 1,556,726 control chromosomes in the GnomAD database, including 26,524 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 0.15 (1803 hom., cov: 32)
  • Exomes 𝑓: 0.18 (24721 hom.)
• Consequence: SLC4A2 NM_003040.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

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]

ENSG00000244151 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC4A2	NM_003040.4	c.3471+55C>T		intron_variant		ENST00000413384.7	NP_003031.3
SLC4A2	NM_001199692.3	c.3471+55C>T		intron_variant			NP_001186621.1
SLC4A2	NM_001199693.1	c.3444+55C>T		intron_variant			NP_001186622.1
SLC4A2	NM_001199694.2	c.3429+55C>T		intron_variant			NP_001186623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC4A2	ENST00000413384.7	c.3471+55C>T		intron_variant		1	NM_003040.4	ENSP00000405600.2

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22256 AN: 152022 Hom.: 1807 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.181 AC: 254811 AN: 1404584 Hom.: 24721 Cov.: 28 AF XY: 0.184 AC XY: 127432 AN XY: 693044

Gnomad4 AFR exome AF: 0.0925

Gnomad4 AMR exome AF: 0.0923

Gnomad4 ASJ exome AF: 0.156

Gnomad4 EAS exome AF: 0.0155

Gnomad4 SAS exome AF: 0.271

Gnomad4 FIN exome AF: 0.134

Gnomad4 NFE exome AF: 0.190

Gnomad4 OTH exome AF: 0.177

GnomAD4 genome AF: 0.146 AC: 22261 AN: 152142 Hom.: 1803 Cov.: 32 AF XY: 0.143 AC XY: 10627 AN XY: 74380

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.147

Alfa AF: 0.161 Hom.: 889

Bravo AF: 0.139

Asia WGS AF: 0.152 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.033
DANN	Benign	0.64

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

Other links and lift over

dbSNP: rs11766855; hg19: chr7-150772917; COSMIC: COSV52540085; COSMIC: COSV52540085;