rs6501683

Positions:

• chr17-74044733-T-C

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02074	ENST00000581028.5	n.512-1224A>G		intron_variant, non_coding_transcript_variant		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;