chr11-64816759-G-A

Variant names:

• chr11-64816759-G-A
• rs470763

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 0.499 in 151,826 control chromosomes in the GnomAD database, including 20,587 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 0.50 (20587 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.597 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: 0.499 AC: 75750 AN: 151706 Hom.: 20578 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.499 AC: 75782 AN: 151826 Hom.: 20587 Cov.: 33 AF XY: 0.499 AC XY: 37042 AN XY: 74212

African (AFR) AF: 0.266 AC: 11003 AN: 41382

American (AMR) AF: 0.592 AC: 9031 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2083 AN: 3464

East Asian (EAS) AF: 0.565 AC: 2911 AN: 5156

South Asian (SAS) AF: 0.441 AC: 2120 AN: 4806

European-Finnish (FIN) AF: 0.558 AC: 5884 AN: 10540

Middle Eastern (MID) AF: 0.538 AC: 155 AN: 288

European-Non Finnish (NFE) AF: 0.602 AC: 40872 AN: 67922

Other (OTH) AF: 0.516 AC: 1086 AN: 2106

Alfa AF: 0.566 Hom.: 24945

Bravo AF: 0.497

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.68
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs470763; hg19: chr11-64584231;