rs10517668

Positions:

• chr4-157436251-T-C

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 0.0892 in 152,226 control chromosomes in the GnomAD database, including 616 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 0.089 (616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 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: 0.0892 AC: 13573 AN: 152108 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0961

Gnomad ASJ AF: 0.0497

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0892

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0892 AC: 13581 AN: 152226 Hom.: 616 Cov.: 32 AF XY: 0.0883 AC XY: 6571 AN XY: 74432

Gnomad4 AFR AF: 0.0808

Gnomad4 AMR AF: 0.0960

Gnomad4 ASJ AF: 0.0497

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0885

Gnomad4 FIN AF: 0.0813

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0869 Hom.: 879

Bravo AF: 0.0906

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517668; hg19: chr4-158357403;