rs1194604

Variant names:

• chr1-154254763-C-A
• rs1194604
• NM_014847.4:c.1855-73C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-154254763-C-A
• chr1-154254763-C-G
• chr1-154254763-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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: G2P, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAP2L	NM_014847.4	MANE Select	c.1855-73C>A		intron	N/A	NP_055662.3
	UBAP2L	NM_001375612.1		c.1888-73C>A		intron	N/A	NP_001362541.1
	UBAP2L	NM_001375614.1		c.1855-73C>A		intron	N/A	NP_001362543.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAP2L	ENST00000428931.6	TSL:5 MANE Select	c.1855-73C>A		intron	N/A	ENSP00000389445.1
	UBAP2L	ENST00000361546.6	TSL:1	c.1855-73C>A		intron	N/A	ENSP00000355343.2
	UBAP2L	ENST00000343815.10	TSL:1	c.1855-73C>A		intron	N/A	ENSP00000345308.6

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

African (AFR) AF: 0.683 AC: 20182 AN: 29534

American (AMR) AF: 0.724 AC: 26344 AN: 36368

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 13615 AN: 24618

East Asian (EAS) AF: 0.969 AC: 37849 AN: 39054

South Asian (SAS) AF: 0.692 AC: 53925 AN: 77938

European-Finnish (FIN) AF: 0.585 AC: 24889 AN: 42514

Middle Eastern (MID) AF: 0.626 AC: 3382 AN: 5400

European-Non Finnish (NFE) AF: 0.557 AC: 559043 AN: 1003588

Other (OTH) AF: 0.614 AC: 33977 AN: 55312

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

African (AFR) AF: 0.673 AC: 27782 AN: 41286

American (AMR) AF: 0.693 AC: 10557 AN: 15242

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

East Asian (EAS) AF: 0.956 AC: 4947 AN: 5172

South Asian (SAS) AF: 0.724 AC: 3491 AN: 4820

European-Finnish (FIN) AF: 0.606 AC: 6249 AN: 10306

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.551 AC: 37387 AN: 67854

Other (OTH) AF: 0.625 AC: 1316 AN: 2104

Alfa AF: 0.571 Hom.: 39806

Bravo AF: 0.633

Asia WGS AF: 0.822 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.7
DANN	Benign	0.72
PhyloP100		-0.045
PromoterAI		0.030	Neutral
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: rs1194604; hg19: chr1-154227239;