11-118384947-TAA-T

Variant names:

• chr11-118384947-TAA-T
• rs370025001
• NM_001204077.2:c.2412+22_2412+23delAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001204077.2(UBE4A):​c.2412+22_2412+23delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,007,182 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0020 (0 hom., cov: 29)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: UBE4A NM_001204077.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.09
• Publications: 1 publications found

Genes affected

UBE4A (HGNC:12499): (ubiquitination factor E4A) This gene encodes a member of the U-box ubiquitin ligase family. The encoded protein is involved in multiubiquitin chain assembly and plays a critical role in chromosome condensation and separation through the polyubiquitination of securin. Autoantibodies against the encoded protein may be markers for scleroderma and Crohn's disease. A pseudogene of this gene is located on the long arm of chromosome 3. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]

UBE4A Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with hypotonia and gross motor and speech delay

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• autosomal recessive non-syndromic intellectual disability

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• multiple congenital anomalies/dysmorphic syndrome

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

LOC100131626 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Variant has high frequency in the EAS (0.167) population. However there is too low homozygotes in high coverage region: (expected more than 4862, got 0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE4A	NM_001204077.2	c.2412+22_2412+23delAA		intron_variant	Intron 15 of 19	ENST00000252108.8	NP_001191006.1
UBE4A	NM_004788.4	c.2433+22_2433+23delAA		intron_variant	Intron 15 of 19		NP_004779.2
LOC100131626	NR_046369.1	n.232-3389_232-3388delTT		intron_variant	Intron 3 of 3
LOC100131626	NR_046370.1	n.232-3442_232-3441delTT		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE4A	ENST00000252108.8	c.2412+3_2412+4delAA		splice_region_variant, intron_variant	Intron 15 of 19	1	NM_001204077.2	ENSP00000252108.4
UBE4A	ENST00000431736.6	c.2433+3_2433+4delAA		splice_region_variant, intron_variant	Intron 15 of 19	1		ENSP00000387362.2
UBE4A	ENST00000545354.1	c.828+3_828+4delAA		splice_region_variant, intron_variant	Intron 6 of 10	2		ENSP00000438918.1

Frequencies

GnomAD3 genomes AF: 0.00204 AC: 162 AN: 79398 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00192

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00188

Gnomad ASJ AF: 0.000501

Gnomad EAS AF: 0.000339

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00152

Gnomad OTH AF: 0.000982

GnomAD2 exomes AF: 0.191 AC: 15984 AN: 83660 AF XY: 0.191

Gnomad AFR exome AF: 0.192

Gnomad AMR exome AF: 0.197

Gnomad ASJ exome AF: 0.182

Gnomad EAS exome AF: 0.204

Gnomad FIN exome AF: 0.199

Gnomad NFE exome AF: 0.187

Gnomad OTH exome AF: 0.186

GnomAD4 exome AF: 0.151 AC: 139794 AN: 927796 Hom.: 0 AF XY: 0.152 AC XY: 71360 AN XY: 470852

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.163 AC: 3429 AN: 21000

American (AMR) AF: 0.153 AC: 3849 AN: 25118

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 2797 AN: 17454

East Asian (EAS) AF: 0.171 AC: 5391 AN: 31588

South Asian (SAS) AF: 0.145 AC: 8294 AN: 57368

European-Finnish (FIN) AF: 0.164 AC: 5111 AN: 31232

Middle Eastern (MID) AF: 0.160 AC: 586 AN: 3664

European-Non Finnish (NFE) AF: 0.148 AC: 103895 AN: 700026

Other (OTH) AF: 0.160 AC: 6442 AN: 40346

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.00204 AC: 162 AN: 79386 Hom.: 0 Cov.: 29 AF XY: 0.00228 AC XY: 86 AN XY: 37712

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00192 AC: 42 AN: 21888

American (AMR) AF: 0.00188 AC: 13 AN: 6898

Ashkenazi Jewish (ASJ) AF: 0.000501 AC: 1 AN: 1998

East Asian (EAS) AF: 0.000341 AC: 1 AN: 2932

South Asian (SAS) AF: 0.00 AC: 0 AN: 2550

European-Finnish (FIN) AF: 0.0113 AC: 47 AN: 4142

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 116

European-Non Finnish (NFE) AF: 0.00152 AC: 57 AN: 37378

Other (OTH) AF: 0.000969 AC: 1 AN: 1032

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 14

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1
Mutation Taster		=88/12	polymorphism

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: rs370025001; hg19: chr11-118255662;