rs361147

Variant names:

• chr4-151969411-G-T
• rs361147
• ENST00000652265.1:n.1355-19742C>A

Variant summary

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

The ENST00000652265.1(ENSG00000286066):​n.1355-19742C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,998 control chromosomes in the GnomAD database, including 19,594 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 0.50 (19594 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000286066 ENST00000652265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

Genes affected

ENSG00000286066 (HGNC:):

LINC03074 (HGNC:56654): (long intergenic non-protein coding RNA 3074)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03074	NR_183803.1	n.*35G>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286066	ENST00000652265.1	n.1355-19742C>A		intron_variant	Intron 1 of 1
ENSG00000286066	ENST00000731965.1	n.211-19742C>A		intron_variant	Intron 1 of 1
ENSG00000286066	ENST00000731966.1	n.375-19742C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75536 AN: 151880 Hom.: 19576 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.511

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.497 AC: 75599 AN: 151998 Hom.: 19594 Cov.: 32 AF XY: 0.488 AC XY: 36223 AN XY: 74284

African (AFR) AF: 0.405 AC: 16789 AN: 41422

American (AMR) AF: 0.500 AC: 7648 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1859 AN: 3472

East Asian (EAS) AF: 0.119 AC: 614 AN: 5164

South Asian (SAS) AF: 0.388 AC: 1868 AN: 4820

European-Finnish (FIN) AF: 0.466 AC: 4926 AN: 10564

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40197 AN: 67942

Other (OTH) AF: 0.516 AC: 1092 AN: 2116

Alfa AF: 0.525 Hom.: 7247

Bravo AF: 0.496

Asia WGS AF: 0.308 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.051
DANN	Benign	0.20
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: rs361147; hg19: chr4-152890563;