chr1-154254763-C-A

Position:

• chr1-154254763-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014847.4(UBAP2L):​c.1855-73C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 1,465,784 control chromosomes in the GnomAD database, including 262,597 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 0.62 (29862 hom., cov: 30)
  • Exomes 𝑓: 0.59 (232735 hom.)
• Consequence: UBAP2L NM_014847.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• 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	Protein	UniProt
UBAP2L	NM_014847.4	c.1855-73C>A		intron_variant		ENST00000428931.6	NP_055662.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBAP2L	ENST00000428931.6	c.1855-73C>A		intron_variant		5	NM_014847.4	ENSP00000389445	A1

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94146 AN: 151344 Hom.: 29844 Cov.: 30

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.628

GnomAD4 exome AF: 0.588 AC: 773206 AN: 1314326 Hom.: 232735 Cov.: 18 AF XY: 0.591 AC XY: 389501 AN XY: 659260

Gnomad4 AFR exome AF: 0.683

Gnomad4 AMR exome AF: 0.724

Gnomad4 ASJ exome AF: 0.553

Gnomad4 EAS exome AF: 0.969

Gnomad4 SAS exome AF: 0.692

Gnomad4 FIN exome AF: 0.585

Gnomad4 NFE exome AF: 0.557

Gnomad4 OTH exome AF: 0.614

GnomAD4 genome AF: 0.622 AC: 94211 AN: 151458 Hom.: 29862 Cov.: 30 AF XY: 0.628 AC XY: 46452 AN XY: 73966

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.625

Alfa AF: 0.563 Hom.: 29972

Bravo AF: 0.633

Asia WGS AF: 0.822 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.7
DANN	Benign	0.72

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: rs1194604; hg19: chr1-154227239;