chr11-64589600-T-C

Variant names:

• chr11-64589600-T-C
• rs505802

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 0.454 in 152,100 control chromosomes in the GnomAD database, including 17,905 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 0.45 (17905 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 75 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 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: 0.454 AC: 68963 AN: 151982 Hom.: 17882 Cov.: 33

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.454 AC: 69044 AN: 152100 Hom.: 17905 Cov.: 33 AF XY: 0.462 AC XY: 34374 AN XY: 74360

African (AFR) AF: 0.682 AC: 28282 AN: 41498

American (AMR) AF: 0.478 AC: 7299 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 994 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4038 AN: 5188

South Asian (SAS) AF: 0.427 AC: 2058 AN: 4818

European-Finnish (FIN) AF: 0.429 AC: 4532 AN: 10570

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20697 AN: 67958

Other (OTH) AF: 0.421 AC: 891 AN: 2116

Alfa AF: 0.355 Hom.: 45658

Bravo AF: 0.468

Asia WGS AF: 0.608 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs505802; hg19: chr11-64357072;