7-151071699-G-T

Variant names:

• chr7-151071699-G-T
• rs2303937
• NM_003040.4:c.2202G>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_003040.4(SLC4A2):​c.2202G>T​(p.Thr734Thr) variant causes a synonymous 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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC4A2 NM_003040.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.15
• Publications: 31 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP7: Synonymous conserved (PhyloP=-5.15 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003040.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC4A2	NM_003040.4	MANE Select	c.2202G>T	p.Thr734Thr	synonymous	Exon 15 of 23	NP_003031.3
	SLC4A2	NM_001199692.3		c.2202G>T	p.Thr734Thr	synonymous	Exon 15 of 23	NP_001186621.1
	SLC4A2	NM_001199693.1		c.2175G>T	p.Thr725Thr	synonymous	Exon 14 of 22	NP_001186622.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC4A2	ENST00000413384.7	TSL:1 MANE Select	c.2202G>T	p.Thr734Thr	synonymous	Exon 15 of 23	ENSP00000405600.2
	SLC4A2	ENST00000485713.6	TSL:1	c.2202G>T	p.Thr734Thr	synonymous	Exon 15 of 23	ENSP00000419412.1
	SLC4A2	ENST00000461735.1	TSL:1	c.2160G>T	p.Thr720Thr	synonymous	Exon 14 of 22	ENSP00000419164.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1456830 Hom.: 0 Cov.: 54 AF XY: 0.00 AC XY: 0 AN XY: 724192

African (AFR) AF: 0.00 AC: 0 AN: 33328

American (AMR) AF: 0.00 AC: 0 AN: 44322

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25832

East Asian (EAS) AF: 0.00 AC: 0 AN: 39618

South Asian (SAS) AF: 0.00 AC: 0 AN: 85962

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53002

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5726

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1108916

Other (OTH) AF: 0.00 AC: 0 AN: 60124

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 27339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.67
DANN	Benign	0.81
PhyloP100		-5.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2303937; hg19: chr7-150768786;