11-64589600-T-C

Variant names:

• chr11-64589600-T-C
• rs505802

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 0.454 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.421

Alfa AF: 0.332 Hom.: 19166

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs505802; hg19: chr11-64357072;