rs10507982

Positions:

• chr13-90585907-G-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 0.11 in 152,090 control chromosomes in the GnomAD database, including 1,719 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 0.11 (1719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 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: 0.110 AC: 16690 AN: 151972 Hom.: 1713 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0977

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

GnomAD4 genome AF: 0.110 AC: 16723 AN: 152090 Hom.: 1719 Cov.: 32 AF XY: 0.111 AC XY: 8223 AN XY: 74358

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.0671

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0546

Gnomad4 NFE AF: 0.0418

Gnomad4 OTH AF: 0.0967

Alfa AF: 0.0804 Hom.: 157

Bravo AF: 0.114

Asia WGS AF: 0.0760 AC: 265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507982; hg19: chr13-91238161;