ENST00000781803.1:n.20G>T

Variant names:

• chr13-85529954-C-A
• rs4482178
• ENST00000781803.1:n.20G>T

Variant summary

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

The ENST00000781803.1(ENSG00000301785):​n.20G>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 0.0848 in 151,772 control chromosomes in the GnomAD database, including 714 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 0.085 (714 hom., cov: 32)
• Consequence: ENSG00000301785 ENST00000781803.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 0 publications found

Genes affected

ENSG00000301785 (HGNC:):

LINC00351 (HGNC:42669): (long intergenic non-protein coding RNA 351)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00351	NR_046989.1	n.494-3122C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301785	ENST00000781803.1	n.20G>T		non_coding_transcript_exon_variant	Exon 1 of 2
LINC00351	ENST00000424926.2	n.496-3122C>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12875 AN: 151654 Hom.: 715 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0713

Gnomad EAS AF: 0.0757

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0848 AC: 12872 AN: 151772 Hom.: 714 Cov.: 32 AF XY: 0.0839 AC XY: 6227 AN XY: 74180

African (AFR) AF: 0.0275 AC: 1140 AN: 41476

American (AMR) AF: 0.162 AC: 2467 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.0713 AC: 247 AN: 3464

East Asian (EAS) AF: 0.0753 AC: 386 AN: 5128

South Asian (SAS) AF: 0.0493 AC: 237 AN: 4812

European-Finnish (FIN) AF: 0.0650 AC: 688 AN: 10590

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7255 AN: 67792

Other (OTH) AF: 0.112 AC: 235 AN: 2104

Alfa AF: 0.104 Hom.: 1233

Bravo AF: 0.0893

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.68
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4482178; hg19: chr13-86104089;