17-74047993-C-T

Variant names:

• chr17-74047993-C-T
• rs8075297
• ENST00000581028.5:n.512-4484G>A

Variant summary

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

The ENST00000581028.5(LINC02074):​n.512-4484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,090 control chromosomes in the GnomAD database, including 42,355 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 (42355 hom., cov: 33)
• Consequence: LINC02074 ENST00000581028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 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.512-4484G>A		intron_variant	Intron 3 of 3	4
LINC02074	ENST00000727554.1	n.353-15547G>A		intron_variant	Intron 3 of 4
LINC02074	ENST00000727555.1	n.512-15547G>A		intron_variant	Intron 3 of 3
LINC02074	ENST00000727570.1	n.120-4484G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113440 AN: 151970 Hom.: 42331 Cov.: 33

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.814

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: 0.772

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: 0.746 AC: 113501 AN: 152090 Hom.: 42355 Cov.: 33 AF XY: 0.741 AC XY: 55059 AN XY: 74346

African (AFR) AF: 0.733 AC: 30412 AN: 41470

American (AMR) AF: 0.732 AC: 11188 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2381 AN: 3470

East Asian (EAS) AF: 0.789 AC: 4065 AN: 5154

South Asian (SAS) AF: 0.732 AC: 3531 AN: 4822

European-Finnish (FIN) AF: 0.682 AC: 7211 AN: 10574

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52164 AN: 68000

Other (OTH) AF: 0.748 AC: 1579 AN: 2112

Alfa AF: 0.720 Hom.: 4218

Bravo AF: 0.748

Asia WGS AF: 0.764 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.42
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs8075297; hg19: chr17-72044132;