rs10517058

chr4-42871198-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 0.0369 in 152,218 control chromosomes in the GnomAD database, including 190 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 0.037 (190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0825 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: 0.0369 AC: 5606 AN: 152100 Hom.: 190 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.0779

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0369 AC: 5614 AN: 152218 Hom.: 190 Cov.: 32 AF XY: 0.0370 AC XY: 2756 AN XY: 74418

Gnomad4 AFR AF: 0.0849

Gnomad4 AMR AF: 0.0188

Gnomad4 ASJ AF: 0.0161

Gnomad4 EAS AF: 0.0298

Gnomad4 SAS AF: 0.0780

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.0162

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0256 Hom.: 29

Bravo AF: 0.0379

Asia WGS AF: 0.0510 AC: 176 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.6
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517058; hg19: chr4-42873215;