rs1107748

Variant names:

• chr17-43696446-T-C
• rs1107748
• ENST00000593169.2:n.196-8983T>C

Variant summary

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

The ENST00000593169.2(LINC02594):​n.196-8983T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,970 control chromosomes in the GnomAD database, including 23,904 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 (23904 hom., cov: 31)
• Consequence: LINC02594 ENST00000593169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 20 publications found

Genes affected

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02594	NR_184089.1	n.289-8983T>C		intron_variant	Intron 3 of 3
LINC02594	NR_184090.1	n.475-8983T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02594	ENST00000593169.2	n.196-8983T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80410 AN: 151852 Hom.: 23863 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.530 AC: 80498 AN: 151970 Hom.: 23904 Cov.: 31 AF XY: 0.529 AC XY: 39270 AN XY: 74282

African (AFR) AF: 0.819 AC: 33933 AN: 41448

American (AMR) AF: 0.481 AC: 7346 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1534 AN: 3466

East Asian (EAS) AF: 0.359 AC: 1847 AN: 5146

South Asian (SAS) AF: 0.438 AC: 2109 AN: 4820

European-Finnish (FIN) AF: 0.471 AC: 4972 AN: 10564

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27362 AN: 67934

Other (OTH) AF: 0.474 AC: 1002 AN: 2114

Alfa AF: 0.438 Hom.: 29738

Bravo AF: 0.544

Asia WGS AF: 0.374 AC: 1303 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	7.0
DANN	Benign	0.70
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs1107748; hg19: chr17-41773814;