rs2207915

Variant names:

• chr20-12209785-A-G
• rs2207915

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 0.178 in 150,606 control chromosomes in the GnomAD database, including 2,631 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 0.18 (2631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26712 AN: 150492 Hom.: 2618 Cov.: 32

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.178 AC: 26762 AN: 150606 Hom.: 2631 Cov.: 32 AF XY: 0.182 AC XY: 13354 AN XY: 73496

African (AFR) AF: 0.0978 AC: 4011 AN: 41014

American (AMR) AF: 0.238 AC: 3566 AN: 14954

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 424 AN: 3460

East Asian (EAS) AF: 0.172 AC: 878 AN: 5090

South Asian (SAS) AF: 0.213 AC: 1018 AN: 4788

European-Finnish (FIN) AF: 0.227 AC: 2363 AN: 10432

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 13974 AN: 67598

Other (OTH) AF: 0.191 AC: 396 AN: 2072

Alfa AF: 0.195 Hom.: 386

Bravo AF: 0.171

Asia WGS AF: 0.228 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.79
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2207915; hg19: chr20-12190433;