14-74763512-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_019589.3(YLPM1):c.23A>G(p.Tyr8Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,338,044 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.000015 (1 hom.)
• Consequence: YLPM1 NM_019589.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.00

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YLPM1	NM_019589.3	c.23A>G	p.Tyr8Cys	missense_variant	1/21	ENST00000325680.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YLPM1	ENST00000325680.12	c.23A>G	p.Tyr8Cys	missense_variant	1/21	5	NM_019589.3	P2
YLPM1	ENST00000552421.5	c.23A>G	p.Tyr8Cys	missense_variant	1/20	5		A2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD3 exomes AF: 0.0000207 AC: 3 AN: 144768 Hom.: 0 AF XY: 0.0000372 AC XY: 3 AN XY: 80574

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000186

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000149 AC: 20 AN: 1338044 Hom.: 1 Cov.: 32 AF XY: 0.0000214 AC XY: 14 AN XY: 655058

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000227

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000191

Gnomad4 OTH exome AF: 0.0000367

GnomAD4 genome Cov.: 31

ExAC AF: 0.0000277 AC: 3

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 22, 2022

The c.23A>G (p.Y8C) alteration is located in exon 1 (coding exon 1) of the YLPM1 gene. This alteration results from a A to G substitution at nucleotide position 23, causing the tyrosine (Y) at amino acid position 8 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.29
Cadd	Pathogenic	26
Dann	Benign	0.97
DEOGEN2	Benign	0.026	T;T
Eigen	Uncertain	0.46
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Benign	0.28	N
LIST_S2	Benign	0.85	D;D
M_CAP	Benign	0.047	D
MetaRNN	Uncertain	0.50	D;D
MetaSVM	Benign	-0.94	T
MutationTaster	Benign	0.52	D;N;N
PrimateAI	Pathogenic	0.88	D
PROVEAN	Benign	-1.7	N;N
REVEL	Benign	0.18
Sift	Pathogenic	0.0	D;.
Sift4G	Uncertain	0.0030	D;D
Vest4		0.79
MutPred		0.27		Gain of catalytic residue at Y8 (P = 0.0026);Gain of catalytic residue at Y8 (P = 0.0026);
MVP		0.043
MPC		0.14
ClinPred		0.48	T
GERP RS		4.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.68
gMVP		0.71

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: rs778679863; hg19: chr14-75230215;