Variant rs957345 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019589.3(YLPM1):c.4522-4C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 1,599,768 control chromosomes in the GnomAD database, including 217,125 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.48 ( 17687 hom., cov: 30)

Exomes 𝑓: 0.52 ( 199438 hom. )

Consequence

YLPM1
NM_019589.3 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00004991

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.138

Variant links:

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]

YLPM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
YLPM1	NM_019589.3 linkuse as main transcript	c.4522-4C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000325680.12	NP_062535.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
YLPM1	ENST00000325680.12 linkuse as main transcript	c.4522-4C>G	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	5	NM_019589.3	ENSP00000324463	P2	P49750-4
YLPM1	ENST00000549293.5 linkuse as main transcript	c.3181-4C>G	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant	1		ENSP00000449860
YLPM1	ENST00000552421.5 linkuse as main transcript	c.2404-4C>G	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	5		ENSP00000447921	A2

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72369

AN:

151788

Hom.:

17670

Cov.:

show subpopulations

Gnomad AFR

AF:

0.363

Gnomad AMI

AF:

0.552

Gnomad AMR

AF:

0.534

Gnomad ASJ

AF:

0.505

Gnomad EAS

AF:

0.544

Gnomad SAS

AF:

0.371

Gnomad FIN

AF:

0.395

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.544

Gnomad OTH

AF:

0.503

GnomAD3 exomes

AF:

0.496

AC:

114557

AN:

230924

Hom.:

28847

AF XY:

0.493

AC XY:

61542

AN XY:

124918

show subpopulations

Gnomad AFR exome

AF:

0.356

Gnomad AMR exome

AF:

0.554

Gnomad ASJ exome

AF:

0.512

Gnomad EAS exome

AF:

0.527

Gnomad SAS exome

AF:

0.382

Gnomad FIN exome

AF:

0.405

Gnomad NFE exome

AF:

0.539

Gnomad OTH exome

AF:

0.524

GnomAD4 exome

AF:

0.521

AC:

754630

AN:

1447860

Hom.:

199438

Cov.:

AF XY:

0.517

AC XY:

372217

AN XY:

719352

show subpopulations

Gnomad4 AFR exome

AF:

0.356

Gnomad4 AMR exome

AF:

0.549

Gnomad4 ASJ exome

AF:

0.508

Gnomad4 EAS exome

AF:

0.495

Gnomad4 SAS exome

AF:

0.388

Gnomad4 FIN exome

AF:

0.418

Gnomad4 NFE exome

AF:

0.541

Gnomad4 OTH exome

AF:

0.522

GnomAD4 genome

AF:

0.477

AC:

72424

AN:

151908

Hom.:

17687

Cov.:

AF XY:

0.469

AC XY:

34824

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.363

Gnomad4 AMR

AF:

0.535

Gnomad4 ASJ

AF:

0.505

Gnomad4 EAS

AF:

0.543

Gnomad4 SAS

AF:

0.373

Gnomad4 FIN

AF:

0.395

Gnomad4 NFE

AF:

0.544

Gnomad4 OTH

AF:

0.502

Alfa

AF:

0.447

Hom.:

2282

Bravo

AF:

0.486

Asia WGS

AF:

0.428

AC:

1491

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

8.2

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000050

dbscSNV1_RF

Benign

0.0

SpliceAI score (max)

0.070

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over