9-82803131-C-T

Variant names:

• chr9-82803131-C-T
• rs10491547

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 0.392 in 151,282 control chromosomes in the GnomAD database, including 11,746 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 0.39 (11746 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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: 0.392 AC: 59306 AN: 151166 Hom.: 11747 Cov.: 30

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.392 AC: 59303 AN: 151282 Hom.: 11746 Cov.: 30 AF XY: 0.392 AC XY: 28962 AN XY: 73830

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.346

Alfa AF: 0.390 Hom.: 1683

Bravo AF: 0.383

Asia WGS AF: 0.365 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.80
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491547; hg19: chr9-85418046;