rs6501683

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-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

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

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.773

Alfa AF: 0.778 Hom.: 80788

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6501683; hg19: chr17-72040872;