rs17836920

chr17-74082787-G-Achr17-74082787-G-Cchr17-74082787-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184084.1(LINC02074):n.511+8235C>T 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 0.299 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 NR_184084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02074	NR_184084.1	n.511+8235C>T		intron_variant, non_coding_transcript_variant
LINC02074	NR_184085.1	n.607+8235C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02074	ENST00000584003.1	n.515+8235C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.281

Alfa AF: 0.326 Hom.: 8803

Bravo AF: 0.289

Asia WGS AF: 0.334 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	7.3
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17836920; hg19: chr17-72078926;