ENST00000690647.2:n.69C>T

Variant names:

• chr1-226348944-C-T
• rs874583
• ENST00000690647.2:n.69C>T

Variant summary

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

The ENST00000690647.2(ENSG00000289348):​n.69C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,866 control chromosomes in the GnomAD database, including 29,959 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 0.62 (29959 hom., cov: 30)
• Consequence: ENSG00000289348 ENST00000690647.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 5 publications found

Genes affected

ENSG00000289348 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690647.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289348	ENST00000690647.2		n.69C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000289348	ENST00000834898.1		n.-231C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94217 AN: 151748 Hom.: 29913 Cov.: 30

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.621 AC: 94321 AN: 151866 Hom.: 29959 Cov.: 30 AF XY: 0.625 AC XY: 46403 AN XY: 74204

African (AFR) AF: 0.698 AC: 28898 AN: 41386

American (AMR) AF: 0.615 AC: 9396 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3470

East Asian (EAS) AF: 0.905 AC: 4652 AN: 5142

South Asian (SAS) AF: 0.651 AC: 3131 AN: 4808

European-Finnish (FIN) AF: 0.646 AC: 6816 AN: 10546

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37863 AN: 67922

Other (OTH) AF: 0.619 AC: 1305 AN: 2108

Alfa AF: 0.576 Hom.: 45434

Bravo AF: 0.624

Asia WGS AF: 0.781 AC: 2715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.52
DANN	Benign	0.74
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs874583; hg19: chr1-226536645;