9-117530056-C-T

Variant names:

• chr9-117530056-C-T
• rs1985317

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 0.482 in 152,032 control chromosomes in the GnomAD database, including 19,786 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 0.48 (19786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

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 = 0.609 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: 0.483 AC: 73300 AN: 151914 Hom.: 19785 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.482 AC: 73316 AN: 152032 Hom.: 19786 Cov.: 32 AF XY: 0.483 AC XY: 35881 AN XY: 74314

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.475

Alfa AF: 0.575 Hom.: 52494

Bravo AF: 0.444

Asia WGS AF: 0.352 AC: 1229 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	3.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1985317; hg19: chr9-120292334;