rs10508136

Positions:

• chr13-104189552-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;