rs1156742

Variant names:

• chr2-49898702-G-A
• rs1156742

Your query was ambiguous. Multiple possible variants found:

• chr2-49898702-G-A
• chr2-49898702-G-C
• chr2-49898702-G-T

Variant summary

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

The variant allele was found at a frequency of 0.541 in 151,884 control chromosomes in the GnomAD database, including 22,688 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 0.54 (22688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82087 AN: 151764 Hom.: 22668 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.541 AC: 82149 AN: 151884 Hom.: 22688 Cov.: 32 AF XY: 0.540 AC XY: 40110 AN XY: 74220

African (AFR) AF: 0.621 AC: 25716 AN: 41420

American (AMR) AF: 0.524 AC: 7993 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3472

East Asian (EAS) AF: 0.442 AC: 2266 AN: 5132

South Asian (SAS) AF: 0.615 AC: 2960 AN: 4812

European-Finnish (FIN) AF: 0.497 AC: 5251 AN: 10556

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33946 AN: 67924

Other (OTH) AF: 0.529 AC: 1118 AN: 2112

Alfa AF: 0.522 Hom.: 32102

Bravo AF: 0.549

Asia WGS AF: 0.525 AC: 1828 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.050
PhyloP100		0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1156742; hg19: chr2-50125840;