rs662760

Positions:

• chr6-85155277-A-C

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 0.127 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0838

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0982

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.142

Alfa AF: 0.131 Hom.: 167

Bravo AF: 0.130

Asia WGS AF: 0.213 AC: 738 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs662760; hg19: chr6-85864995;