Variant 21-42102239-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000408910.7(UMODL1):c.1260T>C(p.Ser420=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 1,612,020 control chromosomes in the GnomAD database, including 237,068 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 0.52 ( 20848 hom., cov: 32)

Exomes 𝑓: 0.54 ( 216220 hom. )

Consequence

UMODL1
ENST00000408910.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.448

Variant links:

Genes affected

UMODL1 (HGNC:12560): (uromodulin like 1) Predicted to be an extracellular matrix structural constituent. Predicted to be involved in neutrophil migration. Predicted to act upstream of or within several processes, including adipose tissue development; cellular response to gonadotropin-releasing hormone; and regulation of ovarian follicle development. Predicted to be located in cytoplasm and external side of plasma membrane. Predicted to be integral component of membrane. Predicted to be active in apical plasma membrane; cell surface; and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

UMODL1 links:

UMODL1-AS1 (HGNC:23821): (UMODL1 antisense RNA 1)

UMODL1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

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

BP7

Synonymous conserved (PhyloP=0.448 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UMODL1	NM_001004416.3 linkuse as main transcript	c.1260T>C	p.Ser420=	synonymous_variant	8/23	ENST00000408910.7	NP_001004416.3
UMODL1-AS1	NR_027243.1 linkuse as main transcript	n.2036A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UMODL1	ENST00000408910.7 linkuse as main transcript	c.1260T>C	p.Ser420=	synonymous_variant	8/23	1	NM_001004416.3	ENSP00000386147	P2	Q5DID0-1
UMODL1-AS1	ENST00000329015.2 linkuse as main transcript	n.2036A>G		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes

AF:

0.522

AC:

79319

AN:

151910

Hom.:

20811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.646

Gnomad AMR

AF:

0.584

Gnomad ASJ

AF:

0.531

Gnomad EAS

AF:

0.569

Gnomad SAS

AF:

0.563

Gnomad FIN

AF:

0.535

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.535

Gnomad OTH

AF:

0.510

GnomAD3 exomes

AF:

0.555

AC:

138340

AN:

249056

Hom.:

38911

AF XY:

0.552

AC XY:

74631

AN XY:

135140

show subpopulations

Gnomad AFR exome

AF:

0.461

Gnomad AMR exome

AF:

0.668

Gnomad ASJ exome

AF:

0.540

Gnomad EAS exome

AF:

0.579

Gnomad SAS exome

AF:

0.549

Gnomad FIN exome

AF:

0.542

Gnomad NFE exome

AF:

0.536

Gnomad OTH exome

AF:

0.561

GnomAD4 exome

AF:

0.543

AC:

793204

AN:

1459994

Hom.:

216220

Cov.:

AF XY:

0.543

AC XY:

394351

AN XY:

726240

show subpopulations

Gnomad4 AFR exome

AF:

0.457

Gnomad4 AMR exome

AF:

0.661

Gnomad4 ASJ exome

AF:

0.537

Gnomad4 EAS exome

AF:

0.601

Gnomad4 SAS exome

AF:

0.556

Gnomad4 FIN exome

AF:

0.541

Gnomad4 NFE exome

AF:

0.539

Gnomad4 OTH exome

AF:

0.534

GnomAD4 genome

AF:

0.522

AC:

79407

AN:

152026

Hom.:

20848

Cov.:

AF XY:

0.524

AC XY:

38912

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.584

Gnomad4 ASJ

AF:

0.531

Gnomad4 EAS

AF:

0.568

Gnomad4 SAS

AF:

0.565

Gnomad4 FIN

AF:

0.535

Gnomad4 NFE

AF:

0.535

Gnomad4 OTH

AF:

0.515

Alfa

AF:

0.538

Hom.:

34246

Bravo

AF:

0.525

Asia WGS

AF:

0.554

AC:

1925

AN:

3478

EpiCase

AF:

0.532

EpiControl

AF:

0.541

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.4

DANN

Benign

0.50

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over