rs4899536

Variant names:

• chr14-74849911-T-C
• rs4899536
• ENST00000554107.2:c.205-5306T>C

Your query was ambiguous. Multiple possible variants found:

• chr14-74849911-T-C
• chr14-74849911-T-G

Variant summary

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

The ENST00000554107.2(YLPM1):​c.205-5306T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 151,922 control chromosomes in the GnomAD database, including 33,877 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 0.65 (33877 hom., cov: 30)
• Consequence: YLPM1 ENST00000554107.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YLPM1	ENST00000554107.2	c.205-5306T>C		intron_variant	Intron 3 of 3	3		ENSP00000476212.1
YLPM1	ENST00000553381.1	n.238-5306T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98386 AN: 151804 Hom.: 33832 Cov.: 30

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.648 AC: 98486 AN: 151922 Hom.: 33877 Cov.: 30 AF XY: 0.651 AC XY: 48302 AN XY: 74250

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.623

Alfa AF: 0.587 Hom.: 4628

Bravo AF: 0.647

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4899536; hg19: chr14-75316614;