9-12675264-T-C

Position:

• chr9-12675264-T-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 0.435 in 151,816 control chromosomes in the GnomAD database, including 18,218 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 0.44 (18218 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 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: 0.435 AC: 66023 AN: 151698 Hom.: 18215 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.435 AC: 66048 AN: 151816 Hom.: 18218 Cov.: 31 AF XY: 0.429 AC XY: 31802 AN XY: 74178

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.436

Alfa AF: 0.573 Hom.: 31284

Bravo AF: 0.398

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10960751; hg19: chr9-12675264;