Variant 14-74763951-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_019589.3(YLPM1):c.462T>A(p.Pro154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,128,358 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0087 ( 4 hom., cov: 17)

Exomes 𝑓: 0.011 ( 72 hom. )

Consequence

YLPM1
NM_019589.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.27

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BP6

Variant 14-74763951-T-A is Benign according to our data. Variant chr14-74763951-T-A is described in ClinVar as [Benign]. Clinvar id is 770997.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.27 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0107 (11066/1032828) while in subpopulation MID AF= 0.023 (80/3472). AF 95% confidence interval is 0.019. There are 72 homozygotes in gnomad4_exome. There are 5440 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
YLPM1	NM_019589.3 linkuse as main transcript	c.462T>A	p.Pro154=	synonymous_variant	1/21	ENST00000325680.12	NP_062535.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
YLPM1	ENST00000325680.12 linkuse as main transcript	c.462T>A	p.Pro154=	synonymous_variant	1/21	5	NM_019589.3	ENSP00000324463	P2	P49750-4
YLPM1	ENST00000552421.5 linkuse as main transcript	c.462T>A	p.Pro154=	synonymous_variant	1/20	5		ENSP00000447921	A2

Frequencies

GnomAD3 genomes

AF:

0.00872

AC:

833

AN:

95478

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00368

Gnomad AMI

AF:

0.00427

Gnomad AMR

AF:

0.0139

Gnomad ASJ

AF:

0.0131

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00361

Gnomad FIN

AF:

0.00681

Gnomad MID

AF:

0.0508

Gnomad NFE

AF:

0.0109

Gnomad OTH

AF:

0.00883

GnomAD3 exomes

AF:

0.00615

AC:

1015

AN:

165022

Hom.:

AF XY:

0.00654

AC XY:

580

AN XY:

88702

show subpopulations

Gnomad AFR exome

AF:

0.00238

Gnomad AMR exome

AF:

0.00422

Gnomad ASJ exome

AF:

0.0108

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00132

Gnomad FIN exome

AF:

0.00240

Gnomad NFE exome

AF:

0.00958

Gnomad OTH exome

AF:

0.00713

GnomAD4 exome

AF:

0.0107

AC:

11066

AN:

1032828

Hom.:

Cov.:

AF XY:

0.0108

AC XY:

5440

AN XY:

503500

show subpopulations

Gnomad4 AFR exome

AF:

0.00256

Gnomad4 AMR exome

AF:

0.00535

Gnomad4 ASJ exome

AF:

0.0197

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00226

Gnomad4 FIN exome

AF:

0.00481

Gnomad4 NFE exome

AF:

0.0119

Gnomad4 OTH exome

AF:

0.0109

GnomAD4 genome

AF:

0.00870

AC:

831

AN:

95530

Hom.:

Cov.:

AF XY:

0.00856

AC XY:

375

AN XY:

43828

show subpopulations

Gnomad4 AFR

AF:

0.00363

Gnomad4 AMR

AF:

0.0139

Gnomad4 ASJ

AF:

0.0131

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00362

Gnomad4 FIN

AF:

0.00681

Gnomad4 NFE

AF:

0.0109

Gnomad4 OTH

AF:

0.00881

Alfa

AF:

0.00672

Hom.:

Bravo

AF:

0.00593

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 13, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.3

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over