17-74047301-C-T

Variant names:

• chr17-74047301-C-T
• rs7213663
• ENST00000581028.5:n.512-3792G>A

Variant summary

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

The ENST00000581028.5(LINC02074):​n.512-3792G>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 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• 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=-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02074	ENST00000581028.5	n.512-3792G>A		intron_variant	Intron 3 of 3	4
LINC02074	ENST00000727554.1	n.353-14855G>A		intron_variant	Intron 3 of 4
LINC02074	ENST00000727555.1	n.512-14855G>A		intron_variant	Intron 3 of 3
LINC02074	ENST00000727570.1	n.120-3792G>A		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.735 AC: 30382 AN: 41342

American (AMR) AF: 0.733 AC: 11170 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2380 AN: 3464

East Asian (EAS) AF: 0.787 AC: 4022 AN: 5108

South Asian (SAS) AF: 0.731 AC: 3506 AN: 4796

European-Finnish (FIN) AF: 0.682 AC: 7134 AN: 10466

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.767 AC: 52133 AN: 67952

Other (OTH) AF: 0.749 AC: 1581 AN: 2112

Alfa AF: 0.755 Hom.: 7587

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs7213663; hg19: chr17-72043440;