rs2241275

Positions:

• chr14-74784737-A-G
• chr14-74784737-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019589.3(YLPM1):​c.2282+2412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,140 control chromosomes in the GnomAD database, including 11,566 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 0.35 (11566 hom., cov: 32)
• Consequence: YLPM1 NM_019589.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YLPM1	NM_019589.3	c.2282+2412A>G		intron_variant		ENST00000325680.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YLPM1	ENST00000325680.12	c.2282+2412A>G		intron_variant		5	NM_019589.3	P2
YLPM1	ENST00000549293.5	c.941+2412A>G		intron_variant, NMD_transcript_variant		1
YLPM1	ENST00000552421.5	c.2282+2412A>G		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53779 AN: 152022 Hom.: 11562 Cov.: 32

Gnomad AFR AF: 0.0936

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.354 AC: 53789 AN: 152140 Hom.: 11566 Cov.: 32 AF XY: 0.351 AC XY: 26100 AN XY: 74352

Gnomad4 AFR AF: 0.0933

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.384

Alfa AF: 0.338 Hom.: 1474

Bravo AF: 0.354

Asia WGS AF: 0.389 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.29
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs2241275; hg19: chr14-75251440;