rs1212352

Variant names:

• chr1-154266807-T-A
• rs1212352
• NM_014847.4:c.2970+239T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-154266807-T-A
• chr1-154266807-T-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 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: Benign. The variant received -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.

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.2970+239T>A		intron	N/A	NP_055662.3
	UBAP2L	NM_001375612.1		c.3003+239T>A		intron	N/A	NP_001362541.1
	UBAP2L	NM_001375614.1		c.2970+239T>A		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.2970+239T>A		intron	N/A	ENSP00000389445.1	Q14157-2
	UBAP2L	ENST00000361546.6	TSL:1	c.2970+239T>A		intron	N/A	ENSP00000355343.2	Q14157-2
	UBAP2L	ENST00000433615.5	TSL:1	c.960+239T>A		intron	N/A	ENSP00000407672.1	H7C2T8

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

African (AFR) AF: 0.843 AC: 34969 AN: 41488

American (AMR) AF: 0.495 AC: 7556 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3468

East Asian (EAS) AF: 0.565 AC: 2922 AN: 5168

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4824

European-Finnish (FIN) AF: 0.651 AC: 6867 AN: 10556

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.600 AC: 40802 AN: 67964

Other (OTH) AF: 0.588 AC: 1239 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.73
PhyloP100		-0.045
Mutation Taster		=100/0	polymorphism (auto)

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: rs1212352; hg19: chr1-154239283;