rs6591765

Variant names:

• chr11-63150781-T-C
• rs6591765

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 0.554 in 151,946 control chromosomes in the GnomAD database, including 25,311 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 0.55 (25311 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.676 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: 0.554 AC: 84125 AN: 151832 Hom.: 25310 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.554 AC: 84138 AN: 151946 Hom.: 25311 Cov.: 31 AF XY: 0.551 AC XY: 40914 AN XY: 74264

African (AFR) AF: 0.324 AC: 13443 AN: 41438

American (AMR) AF: 0.687 AC: 10480 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1573 AN: 3466

East Asian (EAS) AF: 0.348 AC: 1799 AN: 5176

South Asian (SAS) AF: 0.468 AC: 2248 AN: 4808

European-Finnish (FIN) AF: 0.683 AC: 7193 AN: 10538

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45492 AN: 67962

Other (OTH) AF: 0.569 AC: 1199 AN: 2108

Alfa AF: 0.624 Hom.: 27350

Bravo AF: 0.550

Asia WGS AF: 0.427 AC: 1475 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs6591765; hg19: chr11-62918253;