10-116008666-A-G

Position:

• chr10-116008666-A-G

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 0.619 in 152,070 control chromosomes in the GnomAD database, including 31,639 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 0.62 (31639 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 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: 0.619 AC: 94117 AN: 151952 Hom.: 31634 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.619 AC: 94144 AN: 152070 Hom.: 31639 Cov.: 33 AF XY: 0.620 AC XY: 46100 AN XY: 74356

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.618

Alfa AF: 0.678 Hom.: 4575

Bravo AF: 0.601

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180643; hg19: chr10-117768177;