rs2287403

Variant names:

• chr14-74792437-C-T
• rs2287403
• NM_019589.3:c.2283-5143C>T

Variant summary

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

The NM_019589.3(YLPM1):​c.2283-5143C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,136 control chromosomes in the GnomAD database, including 11,707 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 0.36 (11707 hom., cov: 32)
• Consequence: YLPM1 NM_019589.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 5 publications found

Genes affected

YLPM1 (HGNC:17798): (YLP motif containing 1) Enables RNA binding activity. Predicted to be involved in regulation of telomere maintenance. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in cytosol and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YLPM1	NM_019589.3	c.2283-5143C>T		intron_variant	Intron 4 of 20	ENST00000325680.12	NP_062535.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YLPM1	ENST00000325680.12	c.2283-5143C>T		intron_variant	Intron 4 of 20	5	NM_019589.3	ENSP00000324463.7
YLPM1	ENST00000549293.5	n.942-5143C>T		intron_variant	Intron 1 of 16	1		ENSP00000449860.1
YLPM1	ENST00000552421.5	c.2282+10112C>T		intron_variant	Intron 4 of 19	5		ENSP00000447921.1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54241 AN: 152018 Hom.: 11703 Cov.: 32

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.357 AC: 54257 AN: 152136 Hom.: 11707 Cov.: 32 AF XY: 0.354 AC XY: 26355 AN XY: 74366

African (AFR) AF: 0.0983 AC: 4082 AN: 41530

American (AMR) AF: 0.457 AC: 6986 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1608 AN: 3472

East Asian (EAS) AF: 0.540 AC: 2795 AN: 5174

South Asian (SAS) AF: 0.353 AC: 1703 AN: 4822

European-Finnish (FIN) AF: 0.340 AC: 3594 AN: 10568

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32155 AN: 67980

Other (OTH) AF: 0.387 AC: 815 AN: 2104

Alfa AF: 0.408 Hom.: 1738

Bravo AF: 0.357

Asia WGS AF: 0.396 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.42
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2287403; hg19: chr14-75259140;