rs721352

chr9-6332901-A-Cchr9-6332901-A-T

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 0.617 in 152,126 control chromosomes in the GnomAD database, including 31,308 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 0.62 (31308 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93816 AN: 152008 Hom.: 31301 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.617 AC: 93828 AN: 152126 Hom.: 31308 Cov.: 33 AF XY: 0.625 AC XY: 46479 AN XY: 74364

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.625

Alfa AF: 0.675 Hom.: 19605

Bravo AF: 0.603

Asia WGS AF: 0.884 AC: 3070 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	8.3
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: rs721352; hg19: chr9-6332901;