rs6085500

Variant names:

• chr20-6340702-G-A
• rs6085500

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.299 in 152,020 control chromosomes in the GnomAD database, including 6,950 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 0.30 (6950 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45447 AN: 151902 Hom.: 6949 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.299 AC: 45461 AN: 152020 Hom.: 6950 Cov.: 33 AF XY: 0.291 AC XY: 21650 AN XY: 74300

African (AFR) AF: 0.315 AC: 13057 AN: 41476

American (AMR) AF: 0.266 AC: 4065 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1389 AN: 3472

East Asian (EAS) AF: 0.113 AC: 583 AN: 5178

South Asian (SAS) AF: 0.205 AC: 987 AN: 4822

European-Finnish (FIN) AF: 0.271 AC: 2862 AN: 10552

Middle Eastern (MID) AF: 0.410 AC: 119 AN: 290

European-Non Finnish (NFE) AF: 0.316 AC: 21493 AN: 67950

Other (OTH) AF: 0.326 AC: 688 AN: 2110

Alfa AF: 0.291 Hom.: 1357

Bravo AF: 0.298

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	19
DANN	Benign	0.43
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs6085500; hg19: chr20-6321349;