rs17836920

Variant names:

• chr17-74082787-G-A
• rs17836920
• ENST00000581028.5:n.511+8235C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-74082787-G-A
• chr17-74082787-G-C
• chr17-74082787-G-T

Variant summary

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

The ENST00000581028.5(LINC02074):​n.511+8235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,044 control chromosomes in the GnomAD database, including 7,586 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 0.30 (7586 hom., cov: 32)
• Consequence: LINC02074 ENST00000581028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595
• Publications: 3 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 = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581028.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02074	NR_184084.1		n.511+8235C>T		intron	N/A
	LINC02074	NR_184085.1		n.607+8235C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02074	ENST00000581028.5	TSL:4	n.511+8235C>T		intron	N/A
	LINC02074	ENST00000584003.1	TSL:4	n.515+8235C>T		intron	N/A
	LINC02074	ENST00000653467.1		n.610+8235C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45399 AN: 151928 Hom.: 7592 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.299 AC: 45403 AN: 152044 Hom.: 7586 Cov.: 32 AF XY: 0.299 AC XY: 22202 AN XY: 74310

African (AFR) AF: 0.139 AC: 5781 AN: 41498

American (AMR) AF: 0.304 AC: 4644 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 880 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2374 AN: 5154

South Asian (SAS) AF: 0.287 AC: 1381 AN: 4806

European-Finnish (FIN) AF: 0.406 AC: 4282 AN: 10542

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25110 AN: 67964

Other (OTH) AF: 0.281 AC: 593 AN: 2108

Alfa AF: 0.323 Hom.: 11292

Bravo AF: 0.289

Asia WGS AF: 0.334 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.45
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs17836920; hg19: chr17-72078926;