rs2004175

Variant names:

• chr15-39039593-G-T
• rs2004175
• ENST00000560197.5:n.170+31910C>A

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.173+31910C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,014 control chromosomes in the GnomAD database, including 30,260 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 (30260 hom., cov: 32)
• Consequence: ENSG00000259345 ENST00000560484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

ENSG00000259345 (HGNC:):

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

ACMG classification

Verdict is Benign. Variant got -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 = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_007064586.1	n.1445+31910C>A		intron_variant	Intron 3 of 4
LOC105370777	XR_007064587.1	n.1445+31910C>A		intron_variant	Intron 3 of 4
LOC105370777	XR_007064588.1	n.623+31910C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000560197.5	n.170+31910C>A		intron_variant	Intron 2 of 7	5
ENSG00000259345	ENST00000560484.1	n.173+31910C>A		intron_variant	Intron 2 of 3	4
ENSG00000259345	ENST00000561058.5	n.151-21012C>A		intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92038 AN: 151896 Hom.: 30212 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.606 AC: 92147 AN: 152014 Hom.: 30260 Cov.: 32 AF XY: 0.607 AC XY: 45120 AN XY: 74286

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.601

Alfa AF: 0.499 Hom.: 37783

Bravo AF: 0.628

Asia WGS AF: 0.753 AC: 2615 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2004175; hg19: chr15-39331794;