rs10507982

Variant names:

• chr13-90585907-G-A
• rs10507982

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;