17-74047301-C-T

Variant summary

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

The ENST00000581028.5(LINC02074):n.512-3792G>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 0.747 in 151,688 control chromosomes in the GnomAD database, including 42,290 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 0.75 (42290 hom., cov: 29)
• Consequence: LINC02074 ENST00000581028.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

Genes affected

LINC02074 (HGNC:52920): (long intergenic non-protein coding RNA 2074)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02074	ENST00000581028.5	n.512-3792G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113211 AN: 151568 Hom.: 42264 Cov.: 29

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.747 AC: 113274 AN: 151688 Hom.: 42290 Cov.: 29 AF XY: 0.741 AC XY: 54892 AN XY: 74092

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.749

Alfa AF: 0.757 Hom.: 7384

Bravo AF: 0.748

Asia WGS AF: 0.765 AC: 2658 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.2
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7213663; hg19: chr17-72043440;