chr11-64817515-C-T

Variant names:

• chr11-64817515-C-T
• rs2957154

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 0.681 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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.534 AC: 21967 AN: 41132

American (AMR) AF: 0.791 AC: 11979 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2952 AN: 3468

East Asian (EAS) AF: 0.655 AC: 3377 AN: 5156

South Asian (SAS) AF: 0.641 AC: 3063 AN: 4782

European-Finnish (FIN) AF: 0.642 AC: 6683 AN: 10408

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.744 AC: 50538 AN: 67886

Other (OTH) AF: 0.720 AC: 1513 AN: 2102

Alfa AF: 0.730 Hom.: 81955

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
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs2957154; hg19: chr11-64584987;