rs6102085

Positions:

• chr20-40652989-G-A
• chr20-40652989-G-T

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 0.657 in 151,970 control chromosomes in the GnomAD database, including 33,031 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 0.66 (33031 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 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: 0.657 AC: 99713 AN: 151852 Hom.: 32994 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.657 AC: 99799 AN: 151970 Hom.: 33031 Cov.: 31 AF XY: 0.654 AC XY: 48556 AN XY: 74256

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.641

Alfa AF: 0.645 Hom.: 16817

Bravo AF: 0.656

Asia WGS AF: 0.534 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	12
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6102085; hg19: chr20-39281629;