rs10517158

Variant names:

• chr4-29312737-A-G
• rs10517158

Your query was ambiguous. Multiple possible variants found:

• chr4-29312737-A-G
• chr4-29312737-A-T

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 0.163 in 151,606 control chromosomes in the GnomAD database, including 2,430 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 0.16 (2430 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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: 0.163 AC: 24747 AN: 151488 Hom.: 2430 Cov.: 31

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.00292

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.163 AC: 24748 AN: 151606 Hom.: 2430 Cov.: 31 AF XY: 0.159 AC XY: 11805 AN XY: 74058

Gnomad4 AFR AF: 0.0948

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.00293

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.167

Alfa AF: 0.207 Hom.: 4424

Bravo AF: 0.164

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517158; hg19: chr4-29314359;