chr9-27588733-C-A

Variant names:

• chr9-27588733-C-A
• rs702231

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 0.683 in 151,956 control chromosomes in the GnomAD database, including 35,898 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 0.68 (35898 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 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: 0.683 AC: 103729 AN: 151838 Hom.: 35900 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.683 AC: 103758 AN: 151956 Hom.: 35898 Cov.: 31 AF XY: 0.681 AC XY: 50603 AN XY: 74274

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.687

Alfa AF: 0.736 Hom.: 59922

Bravo AF: 0.669

Asia WGS AF: 0.631 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs702231; hg19: chr9-27588731;