chr9-113034273-G-T

Position:

• chr9-113034273-G-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 0.0602 in 152,148 control chromosomes in the GnomAD database, including 308 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 0.060 (308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0829 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: 0.0602 AC: 9150 AN: 152030 Hom.: 308 Cov.: 32

Gnomad AFR AF: 0.0666

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.0900

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0602 AC: 9157 AN: 152148 Hom.: 308 Cov.: 32 AF XY: 0.0609 AC XY: 4531 AN XY: 74368

Gnomad4 AFR AF: 0.0668

Gnomad4 AMR AF: 0.0493

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.0776

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0585 Hom.: 402

Bravo AF: 0.0596

Asia WGS AF: 0.0670 AC: 234 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10981613; hg19: chr9-115796553;