rs10492516

Variant names:

• chr13-74958314-G-A
• rs10492516

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0238 in 151,432 control chromosomes in the GnomAD database, including 109 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 0.024 (109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0907 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: 0.0237 AC: 3590 AN: 151342 Hom.: 108 Cov.: 32

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0772

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00646

Gnomad OTH AF: 0.0216

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

GnomAD4 genome AF: 0.0238 AC: 3597 AN: 151432 Hom.: 109 Cov.: 32 AF XY: 0.0266 AC XY: 1965 AN XY: 73922

African (AFR) AF: 0.0280 AC: 1160 AN: 41360

American (AMR) AF: 0.0772 AC: 1171 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.0162 AC: 56 AN: 3462

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5160

South Asian (SAS) AF: 0.0981 AC: 469 AN: 4782

European-Finnish (FIN) AF: 0.0171 AC: 176 AN: 10296

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.00647 AC: 439 AN: 67900

Other (OTH) AF: 0.0219 AC: 46 AN: 2100

Alfa AF: 0.0161 Hom.: 8

Bravo AF: 0.0266

Asia WGS AF: 0.0670 AC: 231 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.8
DANN	Benign	0.40
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10492516; hg19: chr13-75532451;