2-161039641-T-C

Variant names:

• chr2-161039641-T-C
• rs197275

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 0.869 in 152,196 control chromosomes in the GnomAD database, including 57,517 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 0.87 (57517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.869 AC: 132125 AN: 152078 Hom.: 57480 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.869 AC: 132216 AN: 152196 Hom.: 57517 Cov.: 32 AF XY: 0.868 AC XY: 64584 AN XY: 74388

African (AFR) AF: 0.822 AC: 34123 AN: 41528

American (AMR) AF: 0.889 AC: 13586 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2921 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5164 AN: 5184

South Asian (SAS) AF: 0.867 AC: 4181 AN: 4822

European-Finnish (FIN) AF: 0.859 AC: 9088 AN: 10584

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60464 AN: 68010

Other (OTH) AF: 0.847 AC: 1789 AN: 2112

Alfa AF: 0.882 Hom.: 25823

Bravo AF: 0.871

Asia WGS AF: 0.920 AC: 3193 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.0
DANN	Benign	0.81
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs197275; hg19: chr2-161896152;