chr9-32576999-C-T

Variant names:

• chr9-32576999-C-T
• rs653790

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.200 AC: 8273 AN: 41384

American (AMR) AF: 0.176 AC: 2681 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3470

East Asian (EAS) AF: 0.00504 AC: 26 AN: 5162

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4816

European-Finnish (FIN) AF: 0.216 AC: 2282 AN: 10558

Middle Eastern (MID) AF: 0.193 AC: 56 AN: 290

European-Non Finnish (NFE) AF: 0.237 AC: 16122 AN: 67938

Other (OTH) AF: 0.207 AC: 436 AN: 2110

Alfa AF: 0.223 Hom.: 2048

Bravo AF: 0.200

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.39
PhyloP100		0.30

Splicing

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

Other links and lift over

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