rs1433887

Variant names:

• chr15-38936902-T-C
• rs1433887
• ENST00000560197.6:n.251+37253A>G

Variant summary

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

The ENST00000560197.6(ENSG00000259345):​n.251+37253A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,070 control chromosomes in the GnomAD database, including 14,863 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 0.43 (14863 hom., cov: 33)
• Consequence: ENSG00000259345 ENST00000560197.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 1 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_007064587.1	n.1527-28642A>G		intron_variant	Intron 4 of 4
LOC105370777	XR_007064588.1	n.705-28642A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000560197.6	n.251+37253A>G		intron_variant	Intron 3 of 7	5
ENSG00000259345	ENST00000560484.1	n.254+37253A>G		intron_variant	Intron 3 of 3	4
ENSG00000259345	ENST00000561058.5	n.311+37253A>G		intron_variant	Intron 4 of 5	4

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65619 AN: 151950 Hom.: 14827 Cov.: 33

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.432 AC: 65707 AN: 152070 Hom.: 14863 Cov.: 33 AF XY: 0.427 AC XY: 31743 AN XY: 74340

African (AFR) AF: 0.567 AC: 23499 AN: 41470

American (AMR) AF: 0.344 AC: 5253 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1327 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1243 AN: 5184

South Asian (SAS) AF: 0.312 AC: 1506 AN: 4824

European-Finnish (FIN) AF: 0.380 AC: 4014 AN: 10572

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27598 AN: 67960

Other (OTH) AF: 0.387 AC: 817 AN: 2112

Alfa AF: 0.426 Hom.: 1845

Bravo AF: 0.437

Asia WGS AF: 0.287 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.3
DANN	Benign	0.86
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1433887; hg19: chr15-39229103;