rs10508136

Variant names:

• chr13-104189552-C-A
• rs10508136

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 0.0164 in 152,218 control chromosomes in the GnomAD database, including 82 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 0.016 (82 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910

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 (EAS) allele frequency at 95% confidence interval = 0.0973 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: 0.0164 AC: 2496 AN: 152100 Hom.: 83 Cov.: 33

Gnomad AFR AF: 0.00340

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.00871

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00861

Gnomad OTH AF: 0.0197

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

GnomAD4 genome AF: 0.0164 AC: 2493 AN: 152218 Hom.: 82 Cov.: 33 AF XY: 0.0175 AC XY: 1305 AN XY: 74434

Gnomad4 AFR AF: 0.00339

Gnomad4 AMR AF: 0.0625

Gnomad4 ASJ AF: 0.00547

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.00872

Gnomad4 FIN AF: 0.0157

Gnomad4 NFE AF: 0.00862

Gnomad4 OTH AF: 0.0195

Alfa AF: 0.0104 Hom.: 27

Bravo AF: 0.0214

Asia WGS AF: 0.0510 AC: 175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
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: rs10508136; hg19: chr13-104841902;