13-99432879-T-C

Variant names:

• chr13-99432879-T-C
• rs9517725
• ENST00000646895.1:n.-177A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646895.1(ENSG00000285448):​n.-177A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,216 control chromosomes in the GnomAD database, including 51,117 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 0.81 (51117 hom., cov: 34)
• Consequence: ENSG00000285448 ENST00000646895.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

ENSG00000285448 (HGNC:56890):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.886 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
ENSG00000285448	ENST00000646895.1	n.-177A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123344 AN: 152098 Hom.: 51090 Cov.: 34

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.811 AC: 123425 AN: 152216 Hom.: 51117 Cov.: 34 AF XY: 0.811 AC XY: 60363 AN XY: 74414

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.826

Alfa AF: 0.707 Hom.: 982

Bravo AF: 0.809

Asia WGS AF: 0.832 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9517725; hg19: chr13-100085133;