rs10517702

chr4-159367288-T-Cchr4-159367288-T-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 0.615 in 152,104 control chromosomes in the GnomAD database, including 30,082 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 (30082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

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 (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93488 AN: 151986 Hom.: 30045 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.615 AC: 93585 AN: 152104 Hom.: 30082 Cov.: 32 AF XY: 0.605 AC XY: 44988 AN XY: 74350

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.574

Alfa AF: 0.572 Hom.: 3030

Bravo AF: 0.624

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.4
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517702; hg19: chr4-160288440;