17-43677088-C-T

Variant names:

• chr17-43677088-C-T
• rs8070993
• ENST00000809649.1:n.323-23G>A

Variant summary

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

The ENST00000809649.1(ENSG00000305211):​n.323-23G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,170 control chromosomes in the GnomAD database, including 22,603 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 0.53 (22603 hom., cov: 33)
• Consequence: ENSG00000305211 ENST00000809649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 6 publications found

Genes affected

ENSG00000305211 (HGNC:):

LINC02594 (HGNC:53935): (long intergenic non-protein coding RNA 2594)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809649.1. 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
	LINC02594	NR_184089.1		n.189-3178C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305211	ENST00000809649.1		n.323-23G>A		intron	N/A
	ENSG00000305211	ENST00000809650.1		n.200-23G>A		intron	N/A
	ENSG00000305211	ENST00000809651.1		n.197-23G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79876 AN: 152052 Hom.: 22563 Cov.: 33

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.525 AC: 79958 AN: 152170 Hom.: 22603 Cov.: 33 AF XY: 0.528 AC XY: 39286 AN XY: 74382

African (AFR) AF: 0.747 AC: 31021 AN: 41518

American (AMR) AF: 0.472 AC: 7216 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1306 AN: 3472

East Asian (EAS) AF: 0.512 AC: 2648 AN: 5170

South Asian (SAS) AF: 0.489 AC: 2360 AN: 4826

European-Finnish (FIN) AF: 0.550 AC: 5820 AN: 10590

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28053 AN: 67990

Other (OTH) AF: 0.488 AC: 1029 AN: 2110

Alfa AF: 0.500 Hom.: 3313

Bravo AF: 0.533

Asia WGS AF: 0.471 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs8070993; hg19: chr17-41754456; COSMIC: COSV74166957;