13-38362173-A-G

Position:

• chr13-38362173-A-G

Variant summary

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

The NM_016617.4(UFM1):​c.*1395A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,198 control chromosomes in the GnomAD database, including 59,712 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 0.87 (59704 hom., cov: 31)
  • Exomes 𝑓: 1.0 (8 hom.)
• Consequence: UFM1 NM_016617.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• 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	UniProt
UFM1	NM_016617.4	c.*1395A>G		3_prime_UTR_variant	6/6	ENST00000239878.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UFM1	ENST00000239878.9	c.*1395A>G		3_prime_UTR_variant	6/6	1	NM_016617.4	P1

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132459 AN: 152064 Hom.: 59687 Cov.: 31

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.892

GnomAD4 exome AF: 1.00 AC: 16 AN: 16 Hom.: 8 Cov.: 0 AF XY: 1.00 AC XY: 12 AN XY: 12

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.871 AC: 132515 AN: 152182 Hom.: 59704 Cov.: 31 AF XY: 0.875 AC XY: 65109 AN XY: 74410

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.984

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.893

Alfa AF: 0.925 Hom.: 16613

Bravo AF: 0.857

Asia WGS AF: 0.948 AC: 3297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.0
DANN	Benign	0.86
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2485783; hg19: chr13-38936310;