rs223371

Variant names:

• chr4-102838032-T-A
• rs223371
• NM_181893.3:c.31-28177A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-102838032-T-A
• chr4-102838032-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_181893.3(UBE2D3):​c.31-28177A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: UBE2D3 NM_181893.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

UBE2D3 (HGNC:12476): (ubiquitin conjugating enzyme E2 D3) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme functions in the ubiquitination of the tumor-suppressor protein p53, which is induced by an E3 ubiquitin-protein ligase. [provided by RefSeq, Jan 2017]

UBE2D3-AS1 (HGNC:54095): (UBE2D3 antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2D3	NM_181893.3	c.31-28177A>T		intron_variant	Intron 1 of 6		NP_871622.1
UBE2D3	NM_181890.3	c.-128-11396A>T		intron_variant	Intron 1 of 7		NP_871619.1
UBE2D3-AS1	NR_131185.1	n.187-2677T>A		intron_variant	Intron 1 of 2
UBE2D3-AS1	NR_131186.1	n.132-5292T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2D3	ENST00000357194.10	c.31-28177A>T		intron_variant	Intron 1 of 6	2		ENSP00000349722.6
UBE2D3	ENST00000338145.7	c.-128-11396A>T		intron_variant	Intron 1 of 7	5		ENSP00000337208.3
UBE2D3	ENST00000508238.5	c.-111-11413A>T		intron_variant	Intron 1 of 5	4		ENSP00000423487.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs223371; hg19: chr4-103759189;