rs662760

Variant names:

• chr6-85155277-A-C
• rs662760

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 0.127 in 152,204 control chromosomes in the GnomAD database, including 1,389 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 0.13 (1389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 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: 0.127 AC: 19282 AN: 152086 Hom.: 1387 Cov.: 32

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.127 AC: 19293 AN: 152204 Hom.: 1389 Cov.: 32 AF XY: 0.127 AC XY: 9465 AN XY: 74410

African (AFR) AF: 0.0838 AC: 3482 AN: 41528

American (AMR) AF: 0.147 AC: 2252 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1779 AN: 5168

South Asian (SAS) AF: 0.142 AC: 685 AN: 4820

European-Finnish (FIN) AF: 0.0982 AC: 1041 AN: 10604

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9071 AN: 68018

Other (OTH) AF: 0.142 AC: 300 AN: 2110

Alfa AF: 0.129 Hom.: 169

Bravo AF: 0.130

Asia WGS AF: 0.213 AC: 738 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.67
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs662760; hg19: chr6-85864995;