rs2241275

Variant names:

• chr14-74784737-A-G
• rs2241275
• NM_019589.3:c.2282+2412A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019589.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YLPM1	NM_019589.3	MANE Select	c.2282+2412A>G		intron	N/A	NP_062535.2
	YLPM1	NM_001411052.1		c.2282+2412A>G		intron	N/A	NP_001397981.1	F8VU51

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YLPM1	ENST00000325680.12	TSL:5 MANE Select	c.2282+2412A>G		intron	N/A	ENSP00000324463.7	P49750-4
	YLPM1	ENST00000549293.5	TSL:1	n.941+2412A>G		intron	N/A	ENSP00000449860.1	H0YIQ2
	YLPM1	ENST00000930604.1		c.2276+2412A>G		intron	N/A	ENSP00000600663.1

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

African (AFR) AF: 0.0933 AC: 3876 AN: 41544

American (AMR) AF: 0.454 AC: 6942 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1570 AN: 3464

East Asian (EAS) AF: 0.540 AC: 2796 AN: 5178

South Asian (SAS) AF: 0.344 AC: 1658 AN: 4816

European-Finnish (FIN) AF: 0.338 AC: 3578 AN: 10578

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 32044 AN: 67966

Other (OTH) AF: 0.384 AC: 811 AN: 2112

Alfa AF: 0.329 Hom.: 1480

Bravo AF: 0.354

Asia WGS AF: 0.389 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.29
DANN	Benign	0.60
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2241275; hg19: chr14-75251440;