ENST00000701518.2:n.-96G>A

Variant names:

• chr14-37588860-C-T
• rs12894364
• ENST00000701518.2:n.-96G>A

Variant summary

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

The ENST00000701518.2(ENSG00000289903):​n.-96G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,232 control chromosomes in the GnomAD database, including 639 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 0.078 (639 hom., cov: 33)
• Consequence: ENSG00000289903 ENST00000701518.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.936
• Publications: 2 publications found

Genes affected

ENSG00000289903 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701518.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289903	ENST00000701518.2		n.-96G>A		upstream_gene	N/A
	ENSG00000297171	ENST00000745926.1		n.*8C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 11858 AN: 152114 Hom.: 629 Cov.: 33

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0780 AC: 11879 AN: 152232 Hom.: 639 Cov.: 33 AF XY: 0.0837 AC XY: 6227 AN XY: 74438

African (AFR) AF: 0.0166 AC: 688 AN: 41564

American (AMR) AF: 0.0601 AC: 920 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3472

East Asian (EAS) AF: 0.115 AC: 592 AN: 5170

South Asian (SAS) AF: 0.192 AC: 924 AN: 4818

European-Finnish (FIN) AF: 0.187 AC: 1981 AN: 10586

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0916 AC: 6227 AN: 68004

Other (OTH) AF: 0.0737 AC: 156 AN: 2116

Alfa AF: 0.0845 Hom.: 950

Bravo AF: 0.0642

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.67
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs12894364; hg19: chr14-38058065;