chr9-122115903-C-T

Position:

• chr9-122115903-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 0.0764 in 152,206 control chromosomes in the GnomAD database, including 548 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 0.076 (548 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 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: 0.0764 AC: 11620 AN: 152088 Hom.: 546 Cov.: 33

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0817

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.0696

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0764 AC: 11627 AN: 152206 Hom.: 548 Cov.: 33 AF XY: 0.0778 AC XY: 5788 AN XY: 74414

Gnomad4 AFR AF: 0.0709

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.0696

Gnomad4 FIN AF: 0.0748

Gnomad4 NFE AF: 0.0668

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0523 Hom.: 64

Bravo AF: 0.0776

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.5
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10985535; hg19: chr9-124878182;