9-107674894-C-T

Variant names:

• chr9-107674894-C-T
• rs940287
• ENST00000765079.1:n.-216C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000765079.1(ENSG00000299606):​n.-216C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,062 control chromosomes in the GnomAD database, including 11,769 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 0.37 (11769 hom., cov: 32)
• Consequence: ENSG00000299606 ENST00000765079.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 2 publications found

Genes affected

ENSG00000299606 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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
ENSG00000299606	ENST00000765079.1	n.-216C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56786 AN: 151944 Hom.: 11762 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.374 AC: 56837 AN: 152062 Hom.: 11769 Cov.: 32 AF XY: 0.374 AC XY: 27817 AN XY: 74332

African (AFR) AF: 0.560 AC: 23215 AN: 41466

American (AMR) AF: 0.352 AC: 5378 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3466

East Asian (EAS) AF: 0.448 AC: 2311 AN: 5162

South Asian (SAS) AF: 0.338 AC: 1629 AN: 4818

European-Finnish (FIN) AF: 0.289 AC: 3061 AN: 10578

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18760 AN: 67976

Other (OTH) AF: 0.385 AC: 812 AN: 2110

Alfa AF: 0.358 Hom.: 8683

Bravo AF: 0.391

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs940287; hg19: chr9-110437175; COSMIC: COSV60389089;