7-151069712-A-G

Position:

• chr7-151069712-A-G

Variant summary

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

The NM_003040.4(SLC4A2):​c.1148-235A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,668 control chromosomes in the GnomAD database, including 27,208 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 0.60 (27208 hom., cov: 29)
• Consequence: SLC4A2 NM_003040.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC4A2	NM_003040.4	c.1148-235A>G		intron_variant		ENST00000413384.7	NP_003031.3
SLC4A2	NM_001199692.3	c.1148-235A>G		intron_variant			NP_001186621.1
SLC4A2	NM_001199693.1	c.1121-235A>G		intron_variant			NP_001186622.1
SLC4A2	NM_001199694.2	c.1106-235A>G		intron_variant			NP_001186623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC4A2	ENST00000413384.7	c.1148-235A>G		intron_variant		1	NM_003040.4	ENSP00000405600	P1

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90324 AN: 151550 Hom.: 27183 Cov.: 29

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.596 AC: 90395 AN: 151668 Hom.: 27208 Cov.: 29 AF XY: 0.604 AC XY: 44732 AN XY: 74116

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.612

Alfa AF: 0.590 Hom.: 35482

Bravo AF: 0.599

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.66

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: rs2303933; hg19: chr7-150766799;