chr9-122115903-C-T

Variant names:

• chr9-122115903-C-T
• rs10985535

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;