chr10-17584095-C-A

Variant names:

• chr10-17584095-C-A
• rs4453117

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 0.664 in 152,118 control chromosomes in the GnomAD database, including 35,370 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 0.66 (35370 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 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: 0.664 AC: 100867 AN: 152000 Hom.: 35298 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.664 AC: 100997 AN: 152118 Hom.: 35370 Cov.: 32 AF XY: 0.656 AC XY: 48746 AN XY: 74348

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.654

Alfa AF: 0.450 Hom.: 1116

Bravo AF: 0.683

Asia WGS AF: 0.535 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4453117; hg19: chr10-17626094;