9-31024267-C-T

Variant names:

• chr9-31024267-C-T
• rs10511873

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 0.0301 in 152,312 control chromosomes in the GnomAD database, including 212 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 0.030 (212 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 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: 0.0302 AC: 4590 AN: 152194 Hom.: 213 Cov.: 34

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0301 AC: 4588 AN: 152312 Hom.: 212 Cov.: 34 AF XY: 0.0328 AC XY: 2444 AN XY: 74472

Gnomad4 AFR AF: 0.0189

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.0431

Gnomad4 NFE AF: 0.0155

Gnomad4 OTH AF: 0.0326

Alfa AF: 0.0275 Hom.: 15

Bravo AF: 0.0348

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.59
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511873; hg19: chr9-31024265;