rs1450679

chr9-104264531-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 0.866 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;