rs6591765

Positions:

• chr11-63150781-T-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 0.554 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.569

Alfa AF: 0.624 Hom.: 17196

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6591765; hg19: chr11-62918253;