chr9-32082271-T-C

Variant names:

• chr9-32082271-T-C
• rs10511894

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 0.271 in 152,076 control chromosomes in the GnomAD database, including 5,943 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 0.27 (5943 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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: 0.271 AC: 41126 AN: 151958 Hom.: 5936 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.271 AC: 41146 AN: 152076 Hom.: 5943 Cov.: 33 AF XY: 0.273 AC XY: 20274 AN XY: 74348

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.296

Alfa AF: 0.239 Hom.: 562

Bravo AF: 0.281

Asia WGS AF: 0.393 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511894; hg19: chr9-32082269;