rs181654

Positions:

• chr10-117620145-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 0.627 in 151,876 control chromosomes in the GnomAD database, including 31,184 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 0.63 (31184 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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: 0.627 AC: 95200 AN: 151758 Hom.: 31189 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.627 AC: 95203 AN: 151876 Hom.: 31184 Cov.: 31 AF XY: 0.624 AC XY: 46335 AN XY: 74224

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.674

Alfa AF: 0.667 Hom.: 10699

Bravo AF: 0.617

Asia WGS AF: 0.705 AC: 2447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.89
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs181654; hg19: chr10-119379656;