13-38353751-T-G

Position:

• chr13-38353751-T-G

Variant summary

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

The NM_016617.4(UFM1):​c.60-488T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 151,926 control chromosomes in the GnomAD database, including 56,912 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 0.84 (56912 hom., cov: 30)
• Consequence: UFM1 NM_016617.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

UFM1 (HGNC:20597): (ubiquitin fold modifier 1) UFM1 is a ubiquitin-like protein that is conjugated to target proteins by E1-like activating enzyme UBA5 (UBE1DC1; MIM 610552) and E2-like conjugating enzyme UFC1 (MIM 610554) in a manner analogous to ubiquitylation (see UBE2M; MIM 603173) (Komatsu et al., 2004 [PubMed 15071506]).[supplied by OMIM, Dec 2008]

UFM1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UFM1	NM_016617.4	c.60-488T>G		intron_variant		ENST00000239878.9	NP_057701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UFM1	ENST00000239878.9	c.60-488T>G		intron_variant		1	NM_016617.4	ENSP00000239878.4

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127575 AN: 151808 Hom.: 56901 Cov.: 30

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.840 AC: 127626 AN: 151926 Hom.: 56912 Cov.: 30 AF XY: 0.845 AC XY: 62772 AN XY: 74298

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.875

Alfa AF: 0.886 Hom.: 5437

Bravo AF: 0.823

Asia WGS AF: 0.942 AC: 3273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.75

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: rs2150468; hg19: chr13-38927888;