10-116030653-C-T

Variant names:

• chr10-116030653-C-T
• rs180610

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 0.611 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.367 AC: 15193 AN: 41446

American (AMR) AF: 0.651 AC: 9952 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2656 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1982 AN: 5144

South Asian (SAS) AF: 0.639 AC: 3075 AN: 4814

European-Finnish (FIN) AF: 0.734 AC: 7737 AN: 10544

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.738 AC: 50166 AN: 67984

Other (OTH) AF: 0.599 AC: 1262 AN: 2108

Alfa AF: 0.689 Hom.: 12985

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
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs180610; hg19: chr10-117790164;