17-189133-T-C

Variant names:

• chr17-189133-T-C
• rs7217319
• ENST00000576171.1:n.389-1876A>G

Variant summary

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

The ENST00000792641.1(LINC02091):​n.407-1876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,056 control chromosomes in the GnomAD database, including 28,600 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 0.61 (28600 hom., cov: 33)
• Consequence: LINC02091 ENST00000792641.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 11 publications found

Genes affected

LINC02091 (HGNC:52942): (long intergenic non-protein coding RNA 2091)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792641.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02091	ENST00000576171.1	TSL:5	n.389-1876A>G		intron	N/A
	LINC02091	ENST00000792641.1		n.407-1876A>G		intron	N/A
	LINC02091	ENST00000792642.1		n.512-1876A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92379 AN: 151938 Hom.: 28579 Cov.: 33

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.608 AC: 92441 AN: 152056 Hom.: 28600 Cov.: 33 AF XY: 0.613 AC XY: 45533 AN XY: 74302

African (AFR) AF: 0.516 AC: 21406 AN: 41468

American (AMR) AF: 0.705 AC: 10765 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3468

East Asian (EAS) AF: 0.834 AC: 4322 AN: 5182

South Asian (SAS) AF: 0.675 AC: 3252 AN: 4818

European-Finnish (FIN) AF: 0.661 AC: 6980 AN: 10558

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41747 AN: 67974

Other (OTH) AF: 0.613 AC: 1289 AN: 2104

Alfa AF: 0.609 Hom.: 40162

Bravo AF: 0.608

Asia WGS AF: 0.730 AC: 2538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.84
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs7217319; hg19: chr17-38924;