17-74047731-C-T

Variant names:

• chr17-74047731-C-T
• rs8074960
• ENST00000581028.5:n.512-4222G>A

Variant summary

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

The ENST00000581028.5(LINC02074):​n.512-4222G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,078 control chromosomes in the GnomAD database, including 42,395 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 (42395 hom., cov: 32)
• Consequence: LINC02074 ENST00000581028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02074	ENST00000581028.5	n.512-4222G>A		intron_variant	Intron 3 of 3	4
LINC02074	ENST00000727554.1	n.353-15285G>A		intron_variant	Intron 3 of 4
LINC02074	ENST00000727555.1	n.512-15285G>A		intron_variant	Intron 3 of 3
LINC02074	ENST00000727570.1	n.120-4222G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113477 AN: 151960 Hom.: 42369 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.747 AC: 113540 AN: 152078 Hom.: 42395 Cov.: 32 AF XY: 0.741 AC XY: 55085 AN XY: 74358

African (AFR) AF: 0.735 AC: 30474 AN: 41478

American (AMR) AF: 0.732 AC: 11172 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2382 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4070 AN: 5158

South Asian (SAS) AF: 0.732 AC: 3525 AN: 4814

European-Finnish (FIN) AF: 0.682 AC: 7220 AN: 10590

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52153 AN: 67986

Other (OTH) AF: 0.747 AC: 1576 AN: 2110

Alfa AF: 0.755 Hom.: 7587

Bravo AF: 0.748

Asia WGS AF: 0.766 AC: 2660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs8074960; hg19: chr17-72043870;