11-63018963-C-T

Variant names:

• chr11-63018963-C-T
• rs10792369

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 0.593 in 151,974 control chromosomes in the GnomAD database, including 28,042 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 0.59 (28042 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 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: 0.594 AC: 90147 AN: 151856 Hom.: 28046 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.593 AC: 90168 AN: 151974 Hom.: 28042 Cov.: 31 AF XY: 0.594 AC XY: 44153 AN XY: 74288

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.608

Alfa AF: 0.667 Hom.: 68305

Bravo AF: 0.578

Asia WGS AF: 0.577 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10792369; hg19: chr11-62786435;