chr1-154263533-G-A

Variant names:

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

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>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: G2P, Ambry Genetics

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=-0.36).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBAP2L	NM_014847.4	c.2902+1836G>A		intron_variant	Intron 24 of 26	ENST00000428931.6	NP_055662.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBAP2L	ENST00000428931.6	c.2902+1836G>A		intron_variant	Intron 24 of 26	5	NM_014847.4	ENSP00000389445.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 861328 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 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: 0.00 AC: 0 AN: 780452

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	22
DANN	Benign	0.90
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;