rs2207915

chr20-12209785-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0978

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.191

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2207915; hg19: chr20-12190433;