9-103874752-C-T

Position:

• chr9-103874752-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 0.595 in 151,532 control chromosomes in the GnomAD database, including 27,393 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 0.60 (27393 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 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: 0.595 AC: 90153 AN: 151414 Hom.: 27397 Cov.: 29

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.595 AC: 90170 AN: 151532 Hom.: 27393 Cov.: 29 AF XY: 0.599 AC XY: 44293 AN XY: 73994

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.582

Alfa AF: 0.638 Hom.: 64017

Bravo AF: 0.571

Asia WGS AF: 0.563 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10820559; hg19: chr9-106637033;