chr9-71500428-A-C

Variant names:

• chr9-71500428-A-C
• rs2309966

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;