ENST00000813918.1:n.568T>C

Variant names:

• chr3-30373776-T-C
• rs13316253
• ENST00000813918.1:n.568T>C

Variant summary

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

The ENST00000813918.1(ENSG00000289450):​n.568T>C 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 0.138 in 151,976 control chromosomes in the GnomAD database, including 1,801 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 0.14 (1801 hom., cov: 32)
• Consequence: ENSG00000289450 ENST00000813918.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 1 publications found

Genes affected

ENSG00000289450 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813918.1. 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
	ENSG00000289450	ENST00000813918.1		n.568T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000289450	ENST00000684856.2		n.170+619T>C		intron	N/A
	ENSG00000289450	ENST00000688998.3		n.190+619T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20909 AN: 151858 Hom.: 1792 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.138 AC: 20940 AN: 151976 Hom.: 1801 Cov.: 32 AF XY: 0.142 AC XY: 10518 AN XY: 74286

African (AFR) AF: 0.174 AC: 7216 AN: 41476

American (AMR) AF: 0.266 AC: 4051 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1212 AN: 5138

South Asian (SAS) AF: 0.170 AC: 818 AN: 4822

European-Finnish (FIN) AF: 0.115 AC: 1221 AN: 10580

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0857 AC: 5825 AN: 67952

Other (OTH) AF: 0.120 AC: 254 AN: 2116

Alfa AF: 0.139 Hom.: 315

Bravo AF: 0.154

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.37
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs13316253; hg19: chr3-30415268;