chr9-32601503-C-T

Variant names:

• chr9-32601503-C-T
• rs540467

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 0.283 in 151,970 control chromosomes in the GnomAD database, including 8,066 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 (8066 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 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: 42988 AN: 151852 Hom.: 8030 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.283 AC: 43073 AN: 151970 Hom.: 8066 Cov.: 31 AF XY: 0.277 AC XY: 20553 AN XY: 74266

African (AFR) AF: 0.533 AC: 22096 AN: 41424

American (AMR) AF: 0.188 AC: 2873 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3470

East Asian (EAS) AF: 0.0480 AC: 248 AN: 5170

South Asian (SAS) AF: 0.116 AC: 557 AN: 4820

European-Finnish (FIN) AF: 0.220 AC: 2321 AN: 10542

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13490 AN: 67956

Other (OTH) AF: 0.232 AC: 490 AN: 2110

Alfa AF: 0.212 Hom.: 7618

Bravo AF: 0.292

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.65
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs540467; hg19: chr9-32601501;