Variant 13-38349946-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000239878.9(UFM1):c.2+25A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.954 in 1,614,048 control chromosomes in the GnomAD database, including 740,008 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.87 ( 59484 hom., cov: 31)

Exomes 𝑓: 0.96 ( 680524 hom. )

Consequence

UFM1
ENST00000239878.9 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.181

Variant links:

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 links:

LINC00571 (HGNC:43721): (long intergenic non-protein coding RNA 571)

LINC00571 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 13-38349946-A-T is Benign according to our data. Variant chr13-38349946-A-T is described in ClinVar as [Benign]. Clinvar id is 1684234.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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 linkuse as main transcript	c.2+25A>T		intron_variant		ENST00000239878.9	NP_057701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UFM1	ENST00000239878.9 linkuse as main transcript	c.2+25A>T		intron_variant		1	NM_016617.4	ENSP00000239878	P1	P61960-1
LINC00571	ENST00000454060.2 linkuse as main transcript	n.314T>A		non_coding_transcript_exon_variant	1/8	3

Frequencies

GnomAD3 genomes

AF:

0.869

AC:

132112

AN:

152040

Hom.:

59468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.607

Gnomad AMI

AF:

0.988

Gnomad AMR

AF:

0.937

Gnomad ASJ

AF:

0.935

Gnomad EAS

AF:

0.988

Gnomad SAS

AF:

0.959

Gnomad FIN

AF:

0.983

Gnomad MID

AF:

0.940

Gnomad NFE

AF:

0.973

Gnomad OTH

AF:

0.892

GnomAD3 exomes

AF:

0.946

AC:

237975

AN:

251494

Hom.:

113651

AF XY:

0.953

AC XY:

129479

AN XY:

135920

show subpopulations

Gnomad AFR exome

AF:

0.602

Gnomad AMR exome

AF:

0.966

Gnomad ASJ exome

AF:

0.934

Gnomad EAS exome

AF:

0.987

Gnomad SAS exome

AF:

0.960

Gnomad FIN exome

AF:

0.984

Gnomad NFE exome

AF:

0.972

Gnomad OTH exome

AF:

0.957

GnomAD4 exome

AF:

0.963

AC:

1407975

AN:

1461890

Hom.:

680524

Cov.:

AF XY:

0.964

AC XY:

701002

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.601

Gnomad4 AMR exome

AF:

0.964

Gnomad4 ASJ exome

AF:

0.933

Gnomad4 EAS exome

AF:

0.989

Gnomad4 SAS exome

AF:

0.961

Gnomad4 FIN exome

AF:

0.984

Gnomad4 NFE exome

AF:

0.974

Gnomad4 OTH exome

AF:

0.945

GnomAD4 genome

AF:

0.869

AC:

132167

AN:

152158

Hom.:

59484

Cov.:

AF XY:

0.873

AC XY:

64951

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.607

Gnomad4 AMR

AF:

0.937

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:

0.893

Alfa

AF:

0.921

Hom.:

12047

Bravo

AF:

0.855

Asia WGS

AF:

0.947

AC:

3295

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Leukodystrophy, hypomyelinating, 14

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.2

DANN

Benign

0.59

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over