chr2-20975264-G-A

Variant names:

• chr2-20975264-G-A
• rs6733447

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 0.537 in 151,988 control chromosomes in the GnomAD database, including 22,510 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 (22510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.538 AC: 81648 AN: 151870 Hom.: 22513 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.537 AC: 81663 AN: 151988 Hom.: 22510 Cov.: 32 AF XY: 0.539 AC XY: 40016 AN XY: 74278

African (AFR) AF: 0.446 AC: 18493 AN: 41428

American (AMR) AF: 0.482 AC: 7365 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4438 AN: 5174

South Asian (SAS) AF: 0.719 AC: 3462 AN: 4816

European-Finnish (FIN) AF: 0.520 AC: 5480 AN: 10544

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38222 AN: 67964

Other (OTH) AF: 0.558 AC: 1178 AN: 2110

Alfa AF: 0.537 Hom.: 3808

Bravo AF: 0.528

Asia WGS AF: 0.741 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.011
DANN	Benign	0.74
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6733447; hg19: chr2-21198136;