rs10492604

Positions:

• chr13-58330179-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.14 in 152,210 control chromosomes in the GnomAD database, including 1,806 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 0.14 (1806 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.205 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: 0.140 AC: 21274 AN: 152092 Hom.: 1804 Cov.: 32

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.140 AC: 21284 AN: 152210 Hom.: 1806 Cov.: 32 AF XY: 0.140 AC XY: 10400 AN XY: 74416

Gnomad4 AFR AF: 0.0631

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0507

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.140

Alfa AF: 0.163 Hom.: 4791

Bravo AF: 0.142

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	6.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492604; hg19: chr13-58904313;