rs2309966

Positions:

• chr9-71500428-A-C

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 0.613 in 151,462 control chromosomes in the GnomAD database, including 28,966 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 0.61 (28966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 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: 0.613 AC: 92819 AN: 151344 Hom.: 28927 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.613 AC: 92916 AN: 151462 Hom.: 28966 Cov.: 32 AF XY: 0.608 AC XY: 44984 AN XY: 73968

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.625

Alfa AF: 0.572 Hom.: 32224

Bravo AF: 0.635

Asia WGS AF: 0.564 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2309966; hg19: chr9-74115344;