4-151969411-G-T

Position:

• chr4-151969411-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652265.1(ENSG00000286066):​n.1355-19742C>A variant causes a intron, non coding transcript 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: ENST00000652265.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC03074	NR_183803.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652265.1	n.1355-19742C>A		intron_variant, non_coding_transcript_variant
LINC03074	ENST00000515329.1			downstream_gene_variant		1

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

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

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.516

Alfa AF: 0.543 Hom.: 3685

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs361147; hg19: chr4-152890563;