1-154263533-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_014847.4(UBAP2L):c.2902+1836G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 1,012,292 control chromosomes in the GnomAD database, including 173,539 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 (33401 hom., cov: 32)
  • Exomes 𝑓: 0.57 (140138 hom.)
• Consequence: UBAP2L NM_014847.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBAP2L	NM_014847.4	c.2902+1836G>C		intron_variant		ENST00000428931.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBAP2L	ENST00000428931.6	c.2902+1836G>C		intron_variant		5	NM_014847.4	A1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99100 AN: 151966 Hom.: 33363 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.645

GnomAD4 exome AF: 0.568 AC: 488202 AN: 860208 Hom.: 140138 Cov.: 24 AF XY: 0.567 AC XY: 226355 AN XY: 398998

Gnomad4 AFR exome AF: 0.810

Gnomad4 AMR exome AF: 0.729

Gnomad4 ASJ exome AF: 0.544

Gnomad4 EAS exome AF: 0.956

Gnomad4 SAS exome AF: 0.694

Gnomad4 FIN exome AF: 0.573

Gnomad4 NFE exome AF: 0.555

Gnomad4 OTH exome AF: 0.615

GnomAD4 genome AF: 0.652 AC: 99190 AN: 152084 Hom.: 33401 Cov.: 32 AF XY: 0.657 AC XY: 48848 AN XY: 74332

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.642

Alfa AF: 0.588 Hom.: 3181

Bravo AF: 0.667

Asia WGS AF: 0.831 AC: 2889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	22
Dann	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs1194600; hg19: chr1-154236009;