9-81383431-C-T

Position:

• chr9-81383431-C-T

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 0.288 in 151,904 control chromosomes in the GnomAD database, including 7,456 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 0.29 (7456 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43742 AN: 151788 Hom.: 7463 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.288 AC: 43717 AN: 151904 Hom.: 7456 Cov.: 33 AF XY: 0.292 AC XY: 21641 AN XY: 74220

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.323

Alfa AF: 0.355 Hom.: 7554

Bravo AF: 0.274

Asia WGS AF: 0.300 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332453; hg19: chr9-83998346;