9-1012154-T-C

Position:

• chr9-1012154-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 0.643 in 152,116 control chromosomes in the GnomAD database, including 32,434 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 0.64 (32434 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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: 0.643 AC: 97701 AN: 151998 Hom.: 32393 Cov.: 33

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.643 AC: 97803 AN: 152116 Hom.: 32434 Cov.: 33 AF XY: 0.642 AC XY: 47746 AN XY: 74350

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.589

Alfa AF: 0.594 Hom.: 29477

Bravo AF: 0.642

Asia WGS AF: 0.492 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10738147; hg19: chr9-1012154;