5-172231283-T-C

Variant names:

• chr5-172231283-T-C
• rs9332410
• NM_152277.3:c.307+2839A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152277.3(UBTD2):​c.307+2839A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,040 control chromosomes in the GnomAD database, including 12,278 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 0.40 (12278 hom., cov: 32)
• Consequence: UBTD2 NM_152277.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

UBTD2 (HGNC:24463): (ubiquitin domain containing 2) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBTD2	NM_152277.3	c.307+2839A>G		intron_variant	Intron 2 of 2	ENST00000393792.3	NP_689490.2
UBTD2	XM_017010022.2	c.175+2839A>G		intron_variant	Intron 2 of 2		XP_016865511.1
UBTD2	XM_047417875.1	c.175+2839A>G		intron_variant	Intron 2 of 2		XP_047273831.1
UBTD2	XM_047417876.1	c.175+2839A>G		intron_variant	Intron 3 of 3		XP_047273832.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBTD2	ENST00000393792.3	c.307+2839A>G		intron_variant	Intron 2 of 2	1	NM_152277.3	ENSP00000377381.2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60585 AN: 151922 Hom.: 12269 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.399 AC: 60626 AN: 152040 Hom.: 12278 Cov.: 32 AF XY: 0.405 AC XY: 30134 AN XY: 74326

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.384

Alfa AF: 0.341 Hom.: 2620

Bravo AF: 0.394

Asia WGS AF: 0.491 AC: 1707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332410; hg19: chr5-171658287;