rs1433895

Variant names:

• chr15-38951256-A-G
• rs1433895
• ENST00000560197.6:n.251+22899T>C

Variant summary

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

The ENST00000560197.6(ENSG00000259345):​n.251+22899T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,088 control chromosomes in the GnomAD database, including 12,821 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 0.40 (12821 hom., cov: 33)
• Consequence: ENSG00000259345 ENST00000560197.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 2 publications found

Genes affected

ENSG00000259345 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_007064586.1	n.1527-8972T>C		intron_variant	Intron 4 of 4
LOC105370777	XR_007064587.1	n.1526+22899T>C		intron_variant	Intron 4 of 4
LOC105370777	XR_007064588.1	n.704+22899T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000560197.6	n.251+22899T>C		intron_variant	Intron 3 of 7	5
ENSG00000259345	ENST00000560484.1	n.254+22899T>C		intron_variant	Intron 3 of 3	4
ENSG00000259345	ENST00000561058.5	n.311+22899T>C		intron_variant	Intron 4 of 5	4

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61425 AN: 151970 Hom.: 12805 Cov.: 33

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.404 AC: 61482 AN: 152088 Hom.: 12821 Cov.: 33 AF XY: 0.411 AC XY: 30578 AN XY: 74370

African (AFR) AF: 0.429 AC: 17779 AN: 41466

American (AMR) AF: 0.470 AC: 7176 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3472

East Asian (EAS) AF: 0.599 AC: 3097 AN: 5172

South Asian (SAS) AF: 0.438 AC: 2112 AN: 4820

European-Finnish (FIN) AF: 0.436 AC: 4618 AN: 10584

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23934 AN: 67980

Other (OTH) AF: 0.414 AC: 872 AN: 2108

Alfa AF: 0.372 Hom.: 13034

Bravo AF: 0.408

Asia WGS AF: 0.455 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.63
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1433895; hg19: chr15-39243457;