9-29531581-C-A

Variant names:

• chr9-29531581-C-A
• rs12376718

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 0.237 in 151,990 control chromosomes in the GnomAD database, including 4,616 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 0.24 (4616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 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: 0.237 AC: 36063 AN: 151872 Hom.: 4617 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.0872

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.237 AC: 36068 AN: 151990 Hom.: 4616 Cov.: 32 AF XY: 0.239 AC XY: 17741 AN XY: 74278

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.0876

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.236

Alfa AF: 0.243 Hom.: 2195

Bravo AF: 0.234

Asia WGS AF: 0.151 AC: 523 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	0.36
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12376718; hg19: chr9-29531579;