chr9-104264531-C-T

Variant names:

• chr9-104264531-C-T
• rs1450679

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 0.866 in 152,126 control chromosomes in the GnomAD database, including 57,404 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 0.87 (57404 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.866 AC: 131634 AN: 152008 Hom.: 57363 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.866 AC: 131733 AN: 152126 Hom.: 57404 Cov.: 31 AF XY: 0.864 AC XY: 64218 AN XY: 74358

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.875

Alfa AF: 0.844 Hom.: 62641

Bravo AF: 0.866

Asia WGS AF: 0.858 AC: 2986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	11
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1450679; hg19: chr9-107026812;