10-116030653-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 0.611 in 151,994 control chromosomes in the GnomAD database, including 30,547 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 0.61 (30547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874

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 = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92910 AN: 151876 Hom.: 30539 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.611 AC: 92936 AN: 151994 Hom.: 30547 Cov.: 32 AF XY: 0.612 AC XY: 45423 AN XY: 74256

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.599

Alfa AF: 0.693 Hom.: 7677

Bravo AF: 0.594

Asia WGS AF: 0.510 AC: 1776 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	0.35
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180610; hg19: chr10-117790164;