rs6501683

Variant names:

• chr17-74044733-T-C
• rs6501683
• ENST00000581028.5:n.512-1224A>G

Variant summary

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

The ENST00000581028.5(LINC02074):​n.512-1224A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,068 control chromosomes in the GnomAD database, including 46,284 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 0.78 (46284 hom., cov: 31)
• Consequence: LINC02074 ENST00000581028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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.512-1224A>G		intron_variant	Intron 3 of 3	4
LINC02074	ENST00000727554.1	n.353-12287A>G		intron_variant	Intron 3 of 4
LINC02074	ENST00000727555.1	n.512-12287A>G		intron_variant	Intron 3 of 3
LINC02074	ENST00000727570.1	n.120-1224A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118524 AN: 151948 Hom.: 46233 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.780 AC: 118634 AN: 152068 Hom.: 46284 Cov.: 31 AF XY: 0.774 AC XY: 57529 AN XY: 74298

African (AFR) AF: 0.816 AC: 33862 AN: 41498

American (AMR) AF: 0.791 AC: 12094 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2522 AN: 3466

East Asian (EAS) AF: 0.799 AC: 4126 AN: 5164

South Asian (SAS) AF: 0.735 AC: 3536 AN: 4808

European-Finnish (FIN) AF: 0.682 AC: 7188 AN: 10538

Middle Eastern (MID) AF: 0.781 AC: 228 AN: 292

European-Non Finnish (NFE) AF: 0.775 AC: 52708 AN: 67992

Other (OTH) AF: 0.773 AC: 1627 AN: 2106

Alfa AF: 0.779 Hom.: 187062

Bravo AF: 0.789

Asia WGS AF: 0.782 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.9
DANN	Benign	0.69
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs6501683; hg19: chr17-72040872;