chr9-32163681-C-T

Variant names:

• chr9-32163681-C-T
• rs10738881

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 0.694 in 152,016 control chromosomes in the GnomAD database, including 36,690 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 0.69 (36690 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.715 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: 0.694 AC: 105472 AN: 151898 Hom.: 36651 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.694 AC: 105571 AN: 152016 Hom.: 36690 Cov.: 31 AF XY: 0.693 AC XY: 51456 AN XY: 74302

African (AFR) AF: 0.678 AC: 28102 AN: 41444

American (AMR) AF: 0.726 AC: 11093 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2189 AN: 3468

East Asian (EAS) AF: 0.662 AC: 3424 AN: 5170

South Asian (SAS) AF: 0.616 AC: 2956 AN: 4802

European-Finnish (FIN) AF: 0.672 AC: 7093 AN: 10550

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.713 AC: 48453 AN: 67996

Other (OTH) AF: 0.686 AC: 1447 AN: 2110

Alfa AF: 0.703 Hom.: 16816

Bravo AF: 0.695

Asia WGS AF: 0.661 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs10738881; hg19: chr9-32163679;