chr1-154263533-G-T

Variant names:

• chr1-154263533-G-T
• rs1194600
• NM_014847.4:c.2902+1836G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_014847.4(UBAP2L):​c.2902+1836G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000116 in 861,328 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000012 (0 hom.)
• Consequence: UBAP2L NM_014847.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 4 publications found

Genes affected

UBAP2L (HGNC:29877): (ubiquitin associated protein 2 like) Enables RNA binding activity. Involved in binding activity of sperm to zona pellucida and stress granule assembly. Acts upstream of or within hematopoietic stem cell homeostasis. Part of PcG protein complex. [provided by Alliance of Genome Resources, Apr 2022]

UBAP2L Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic facies

  Inheritance: AD Classification: DEFINITIVE, MODERATE Submitted by: Ambry Genetics, G2P

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014847.4. 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
	UBAP2L	NM_014847.4	MANE Select	c.2902+1836G>T		intron	N/A	NP_055662.3
	UBAP2L	NM_001375612.1		c.2935+1836G>T		intron	N/A	NP_001362541.1
	UBAP2L	NM_001375614.1		c.2902+1836G>T		intron	N/A	NP_001362543.1	Q14157-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAP2L	ENST00000428931.6	TSL:5 MANE Select	c.2902+1836G>T		intron	N/A	ENSP00000389445.1	Q14157-2
	UBAP2L	ENST00000361546.6	TSL:1	c.2902+1836G>T		intron	N/A	ENSP00000355343.2	Q14157-2
	UBAP2L	ENST00000433615.5	TSL:1	c.892+1836G>T		intron	N/A	ENSP00000407672.1	H7C2T8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000116 AC: 1 AN: 861328 Hom.: 0 Cov.: 24 AF XY: 0.00000250 AC XY: 1 AN XY: 399514

African (AFR) AF: 0.00 AC: 0 AN: 16682

American (AMR) AF: 0.00 AC: 0 AN: 1704

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6212

East Asian (EAS) AF: 0.00 AC: 0 AN: 5212

South Asian (SAS) AF: 0.00 AC: 0 AN: 18280

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1836

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1752

European-Non Finnish (NFE) AF: 0.00000128 AC: 1 AN: 780452

Other (OTH) AF: 0.00 AC: 0 AN: 29198

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 3181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	21
DANN	Benign	0.82
PhyloP100		1.4

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

Other links and lift over

dbSNP: rs1194600; hg19: chr1-154236009;