11-64817515-C-T

Position:

• chr11-64817515-C-T

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 0.681 in 151,272 control chromosomes in the GnomAD database, including 35,838 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 0.68 (35838 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.78 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: 0.681 AC: 102943 AN: 151154 Hom.: 35819 Cov.: 28

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.681 AC: 103014 AN: 151272 Hom.: 35838 Cov.: 28 AF XY: 0.677 AC XY: 49965 AN XY: 73826

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.720

Alfa AF: 0.738 Hom.: 57285

Bravo AF: 0.687

Asia WGS AF: 0.615 AC: 2140 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	0.44
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2957154; hg19: chr11-64584987;