chr9-107386275-T-C

Position:

• chr9-107386275-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 0.659 in 151,992 control chromosomes in the GnomAD database, including 33,727 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 0.66 (33727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 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: 0.659 AC: 100132 AN: 151872 Hom.: 33704 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.659 AC: 100191 AN: 151992 Hom.: 33727 Cov.: 32 AF XY: 0.660 AC XY: 48998 AN XY: 74280

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.659

Alfa AF: 0.693 Hom.: 4584

Bravo AF: 0.653

Asia WGS AF: 0.571 AC: 1987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.3
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1746825; hg19: chr9-110148556;