chr1-154266807-T-A

Position:

• chr1-154266807-T-A

Variant summary

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

The NM_014847.4(UBAP2L):​c.2970+239T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,036 control chromosomes in the GnomAD database, including 33,633 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 (33633 hom., cov: 31)
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBAP2L	NM_014847.4	c.2970+239T>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.2970+239T>A		intron_variant		5	NM_014847.4	ENSP00000389445	A1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99098 AN: 151920 Hom.: 33587 Cov.: 31

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.584

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.652 AC: 99197 AN: 152036 Hom.: 33633 Cov.: 31 AF XY: 0.648 AC XY: 48187 AN XY: 74326

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.588

Alfa AF: 0.602 Hom.: 15448

Bravo AF: 0.647

Asia WGS AF: 0.553 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.73

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: rs1212352; hg19: chr1-154239283;