chr9-32576999-C-T

Variant names:

• chr9-32576999-C-T
• rs653790

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 0.204 in 151,904 control chromosomes in the GnomAD database, including 3,346 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 0.20 (3346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 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: 0.204 AC: 31036 AN: 151786 Hom.: 3345 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00503

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.204 AC: 31036 AN: 151904 Hom.: 3346 Cov.: 32 AF XY: 0.201 AC XY: 14926 AN XY: 74202

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.00504

Gnomad4 SAS AF: 0.0959

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.207

Alfa AF: 0.223 Hom.: 1839

Bravo AF: 0.200

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs653790; hg19: chr9-32576997; COSMIC: COSV63083209;