1-154263533-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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: Ambry Genetics, G2P

ACMG classification

Our verdict: Benign. The variant received -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.

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.2902+1836G>C		intron	N/A	NP_055662.3
	UBAP2L	NM_001375612.1		c.2935+1836G>C		intron	N/A	NP_001362541.1
	UBAP2L	NM_001375614.1		c.2902+1836G>C		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.2902+1836G>C		intron	N/A	ENSP00000389445.1	Q14157-2
	UBAP2L	ENST00000361546.6	TSL:1	c.2902+1836G>C		intron	N/A	ENSP00000355343.2	Q14157-2
	UBAP2L	ENST00000433615.5	TSL:1	c.892+1836G>C		intron	N/A	ENSP00000407672.1	H7C2T8

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

African (AFR) AF: 0.810 AC: 13502 AN: 16670

American (AMR) AF: 0.729 AC: 1240 AN: 1702

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 3368 AN: 6194

East Asian (EAS) AF: 0.956 AC: 4983 AN: 5212

South Asian (SAS) AF: 0.694 AC: 12660 AN: 18250

European-Finnish (FIN) AF: 0.573 AC: 1049 AN: 1830

Middle Eastern (MID) AF: 0.632 AC: 1105 AN: 1748

European-Non Finnish (NFE) AF: 0.555 AC: 432377 AN: 779460

Other (OTH) AF: 0.615 AC: 17918 AN: 29142

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

African (AFR) AF: 0.780 AC: 32364 AN: 41502

American (AMR) AF: 0.701 AC: 10712 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3470

East Asian (EAS) AF: 0.957 AC: 4959 AN: 5184

South Asian (SAS) AF: 0.724 AC: 3496 AN: 4826

European-Finnish (FIN) AF: 0.605 AC: 6383 AN: 10542

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37434 AN: 67954

Other (OTH) AF: 0.642 AC: 1359 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	22
DANN	Benign	0.77
PhyloP100		1.4
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: rs1194600; hg19: chr1-154236009;