ENST00000793037.1:n.378C>T

Variant names:

• chr13-110515070-G-A
• rs873294
• ENST00000793037.1:n.378C>T

Variant summary

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

The ENST00000793037.1(ENSG00000289010):​n.378C>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 0.188 in 152,196 control chromosomes in the GnomAD database, including 3,148 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 0.19 (3148 hom., cov: 32)
• Consequence: ENSG00000289010 ENST00000793037.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 2 publications found

Genes affected

ENSG00000289010 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793037.1. 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
	ENSG00000289010	ENST00000793037.1		n.378C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000289010	ENST00000793038.1		n.269C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000289010	ENST00000793035.1		n.150+5680C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28545 AN: 152076 Hom.: 3145 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.188 AC: 28577 AN: 152196 Hom.: 3148 Cov.: 32 AF XY: 0.195 AC XY: 14480 AN XY: 74402

African (AFR) AF: 0.0794 AC: 3299 AN: 41552

American (AMR) AF: 0.204 AC: 3114 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2230 AN: 5146

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4830

European-Finnish (FIN) AF: 0.296 AC: 3132 AN: 10586

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14269 AN: 68000

Other (OTH) AF: 0.172 AC: 364 AN: 2116

Alfa AF: 0.201 Hom.: 10567

Bravo AF: 0.177

Asia WGS AF: 0.317 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs873294; hg19: chr13-111167417;