chr2-20976028-G-A

Variant names:

• chr2-20976028-G-A
• rs11902417

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 0.255 in 152,098 control chromosomes in the GnomAD database, including 5,842 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 0.26 (5842 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38797 AN: 151980 Hom.: 5844 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.255 AC: 38804 AN: 152098 Hom.: 5842 Cov.: 33 AF XY: 0.262 AC XY: 19445 AN XY: 74336

African (AFR) AF: 0.199 AC: 8250 AN: 41502

American (AMR) AF: 0.233 AC: 3566 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3735 AN: 5156

South Asian (SAS) AF: 0.525 AC: 2525 AN: 4812

European-Finnish (FIN) AF: 0.272 AC: 2879 AN: 10568

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16053 AN: 68004

Other (OTH) AF: 0.255 AC: 538 AN: 2110

Alfa AF: 0.258 Hom.: 12045

Bravo AF: 0.249

Asia WGS AF: 0.587 AC: 2039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.56
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11902417; hg19: chr2-21198900;