rs2182710

Variant names:

• chr20-6382560-T-C
• rs2182710

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 0.716 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.716 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

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.740

Alfa AF: 0.657 Hom.: 9386

Bravo AF: 0.735

Asia WGS AF: 0.764 AC: 2658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2182710; hg19: chr20-6363207;