rs6085729

Variant names:

• chr20-6921524-T-C
• rs6085729

Your query was ambiguous. Multiple possible variants found:

• chr20-6921524-T-C
• chr20-6921524-T-G

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 0.683 in 152,116 control chromosomes in the GnomAD database, including 35,952 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 0.68 (35952 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.735 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: 0.683 AC: 103848 AN: 151998 Hom.: 35952 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.683 AC: 103883 AN: 152116 Hom.: 35952 Cov.: 33 AF XY: 0.683 AC XY: 50763 AN XY: 74360

African (AFR) AF: 0.578 AC: 23958 AN: 41456

American (AMR) AF: 0.679 AC: 10371 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2516 AN: 3472

East Asian (EAS) AF: 0.546 AC: 2822 AN: 5172

South Asian (SAS) AF: 0.699 AC: 3371 AN: 4824

European-Finnish (FIN) AF: 0.761 AC: 8047 AN: 10578

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50336 AN: 68018

Other (OTH) AF: 0.686 AC: 1451 AN: 2116

Alfa AF: 0.707 Hom.: 4748

Bravo AF: 0.672

Asia WGS AF: 0.619 AC: 2151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.4
DANN	Benign	0.61
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs6085729; hg19: chr20-6902171;