14-74792437-C-T

Position:

• chr14-74792437-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
YLPM1	NM_019589.3	c.2283-5143C>T		intron_variant		ENST00000325680.12	NP_062535.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
YLPM1	ENST00000325680.12	c.2283-5143C>T		intron_variant		5	NM_019589.3	ENSP00000324463	P2
YLPM1	ENST00000549293.5	c.942-5143C>T		intron_variant, NMD_transcript_variant		1		ENSP00000449860
YLPM1	ENST00000552421.5	c.2282+10112C>T		intron_variant		5		ENSP00000447921	A2

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

Gnomad4 AFR AF: 0.0983

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.387

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2287403; hg19: chr14-75259140;