chr9-130502523-C-T

Variant names:

• chr9-130502523-C-T
• rs10793902

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 0.519 in 151,916 control chromosomes in the GnomAD database, including 21,037 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 0.52 (21037 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 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: 0.520 AC: 78869 AN: 151798 Hom.: 21035 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.519 AC: 78887 AN: 151916 Hom.: 21037 Cov.: 31 AF XY: 0.524 AC XY: 38897 AN XY: 74244

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.551

Alfa AF: 0.569 Hom.: 36369

Bravo AF: 0.498

Asia WGS AF: 0.404 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10793902; hg19: chr9-133377910; COSMIC: COSV61688830;