10-118637619-A-G

Position:

• chr10-118637619-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 0.561 in 152,046 control chromosomes in the GnomAD database, including 24,132 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 0.56 (24132 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.846

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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: 0.561 AC: 85272 AN: 151926 Hom.: 24133 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.561 AC: 85298 AN: 152046 Hom.: 24132 Cov.: 32 AF XY: 0.564 AC XY: 41930 AN XY: 74312

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.558

Alfa AF: 0.561 Hom.: 4867

Bravo AF: 0.561

Asia WGS AF: 0.634 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4752182; hg19: chr10-120397131;