rs2182710

Variant names:

• chr20-6382560-T-C
• rs2182710

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 0.716 in 151,922 control chromosomes in the GnomAD database, including 40,224 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 0.72 (40224 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 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: 0.716 AC: 108721 AN: 151804 Hom.: 40168 Cov.: 29

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.716 AC: 108838 AN: 151922 Hom.: 40224 Cov.: 29 AF XY: 0.716 AC XY: 53172 AN XY: 74240

African (AFR) AF: 0.892 AC: 37004 AN: 41464

American (AMR) AF: 0.724 AC: 11058 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3470

East Asian (EAS) AF: 0.884 AC: 4563 AN: 5164

South Asian (SAS) AF: 0.655 AC: 3132 AN: 4780

European-Finnish (FIN) AF: 0.653 AC: 6897 AN: 10556

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41416 AN: 67904

Other (OTH) AF: 0.740 AC: 1564 AN: 2114

Alfa AF: 0.654 Hom.: 16990

Bravo AF: 0.735

Asia WGS AF: 0.764 AC: 2658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.32
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2182710; hg19: chr20-6363207;