13-87982335-C-G

Variant names:

• chr13-87982335-C-G
• rs10492674

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 0.483 in 151,932 control chromosomes in the GnomAD database, including 20,546 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 0.48 (20546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 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: 0.482 AC: 73243 AN: 151812 Hom.: 20516 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.483 AC: 73318 AN: 151932 Hom.: 20546 Cov.: 32 AF XY: 0.480 AC XY: 35650 AN XY: 74234

African (AFR) AF: 0.784 AC: 32539 AN: 41488

American (AMR) AF: 0.371 AC: 5659 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1826 AN: 5152

South Asian (SAS) AF: 0.525 AC: 2531 AN: 4822

European-Finnish (FIN) AF: 0.340 AC: 3583 AN: 10538

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24138 AN: 67906

Other (OTH) AF: 0.467 AC: 982 AN: 2104

Alfa AF: 0.218 Hom.: 411

Bravo AF: 0.494

Asia WGS AF: 0.436 AC: 1518 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.35
DANN	Benign	0.42
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10492674; hg19: chr13-88634590;