chr9-32590580-C-T

Variant names:

• chr9-32590580-C-T
• rs10971037

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 0.29 in 152,060 control chromosomes in the GnomAD database, including 8,589 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 0.29 (8589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44012 AN: 151942 Hom.: 8549 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.290 AC: 44103 AN: 152060 Hom.: 8589 Cov.: 32 AF XY: 0.283 AC XY: 21057 AN XY: 74378

African (AFR) AF: 0.557 AC: 23065 AN: 41422

American (AMR) AF: 0.189 AC: 2886 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3468

East Asian (EAS) AF: 0.0532 AC: 276 AN: 5184

South Asian (SAS) AF: 0.118 AC: 570 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2352 AN: 10592

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13449 AN: 67970

Other (OTH) AF: 0.240 AC: 507 AN: 2114

Alfa AF: 0.199 Hom.: 1599

Bravo AF: 0.299

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10971037; hg19: chr9-32590578; COSMIC: COSV70619133;