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. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554107.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YLPM1	ENST00000554107.2	TSL:3	c.205-5306T>C		intron	N/A	ENSP00000476212.1
	YLPM1	ENST00000553381.1	TSL:3	n.238-5306T>C		intron	N/A

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

African (AFR) AF: 0.903 AC: 37417 AN: 41454

American (AMR) AF: 0.548 AC: 8370 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1892 AN: 3464

East Asian (EAS) AF: 0.461 AC: 2378 AN: 5162

South Asian (SAS) AF: 0.677 AC: 3255 AN: 4808

European-Finnish (FIN) AF: 0.662 AC: 6971 AN: 10536

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36202 AN: 67926

Other (OTH) AF: 0.623 AC: 1309 AN: 2102

Alfa AF: 0.596 Hom.: 4945

Bravo AF: 0.647

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.33
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs4899536; hg19: chr14-75316614;