9-119676531-A-T

Variant names:

• chr9-119676531-A-T
• rs17582214

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 0.283 in 152,100 control chromosomes in the GnomAD database, including 6,705 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 0.28 (6705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.418 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: 0.283 AC: 43010 AN: 151982 Hom.: 6710 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.283 AC: 43006 AN: 152100 Hom.: 6705 Cov.: 32 AF XY: 0.285 AC XY: 21185 AN XY: 74342

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.290

Alfa AF: 0.197 Hom.: 472

Bravo AF: 0.273

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17582214; hg19: chr9-122438809;