9-123294185-C-T

Position:

• chr9-123294185-C-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 0.341 in 151,544 control chromosomes in the GnomAD database, including 9,549 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 0.34 (9549 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51602 AN: 151430 Hom.: 9537 Cov.: 27

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.341 AC: 51645 AN: 151544 Hom.: 9549 Cov.: 27 AF XY: 0.338 AC XY: 25035 AN XY: 73994

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.303

Alfa AF: 0.399 Hom.: 16848

Bravo AF: 0.322

Asia WGS AF: 0.255 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10818803; hg19: chr9-126056464;