Variant rs220158 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001004416.3(UMODL1):c.3537T>C(p.Pro1179=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 1,613,138 control chromosomes in the GnomAD database, including 643,911 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. Synonymous variant affecting the same amino acid position (i.e. P1179P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.86 ( 56556 hom., cov: 32)

Exomes 𝑓: 0.90 ( 587355 hom. )

Consequence

UMODL1
NM_001004416.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.46

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:

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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=-1.0).

BP7

Synonymous conserved (PhyloP=-4.45 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UMODL1	NM_001004416.3 linkuse as main transcript	c.3537T>C	p.Pro1179=	synonymous_variant	20/23	ENST00000408910.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMODL1	ENST00000408910.7 linkuse as main transcript	c.3537T>C	p.Pro1179=	synonymous_variant	20/23	1	NM_001004416.3	P2	Q5DID0-1

Frequencies

GnomAD3 genomes

AF:

0.860

AC:

130783

AN:

152050

Hom.:

56528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.782

Gnomad AMI

AF:

0.940

Gnomad AMR

AF:

0.877

Gnomad ASJ

AF:

0.959

Gnomad EAS

AF:

0.775

Gnomad SAS

AF:

0.801

Gnomad FIN

AF:

0.862

Gnomad MID

AF:

0.968

Gnomad NFE

AF:

0.908

Gnomad OTH

AF:

0.867

GnomAD3 exomes

AF:

0.875

AC:

217320

AN:

248258

Hom.:

95523

AF XY:

0.876

AC XY:

117962

AN XY:

134664

show subpopulations

Gnomad AFR exome

AF:

0.779

Gnomad AMR exome

AF:

0.879

Gnomad ASJ exome

AF:

0.969

Gnomad EAS exome

AF:

0.781

Gnomad SAS exome

AF:

0.814

Gnomad FIN exome

AF:

0.866

Gnomad NFE exome

AF:

0.911

Gnomad OTH exome

AF:

0.895

GnomAD4 exome

AF:

0.896

AC:

1308627

AN:

1460970

Hom.:

587355

Cov.:

AF XY:

0.894

AC XY:

649946

AN XY:

726784

show subpopulations

Gnomad4 AFR exome

AF:

0.777

Gnomad4 AMR exome

AF:

0.881

Gnomad4 ASJ exome

AF:

0.967

Gnomad4 EAS exome

AF:

0.779

Gnomad4 SAS exome

AF:

0.821

Gnomad4 FIN exome

AF:

0.868

Gnomad4 NFE exome

AF:

0.910

Gnomad4 OTH exome

AF:

0.891

GnomAD4 genome

AF:

0.860

AC:

130867

AN:

152168

Hom.:

56556

Cov.:

AF XY:

0.855

AC XY:

63595

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.781

Gnomad4 AMR

AF:

0.877

Gnomad4 ASJ

AF:

0.959

Gnomad4 EAS

AF:

0.775

Gnomad4 SAS

AF:

0.801

Gnomad4 FIN

AF:

0.862

Gnomad4 NFE

AF:

0.908

Gnomad4 OTH

AF:

0.864

Alfa

AF:

0.902

Hom.:

60545

Bravo

AF:

0.859

Asia WGS

AF:

0.784

AC:

2729

AN:

3478

EpiCase

AF:

0.917

EpiControl

AF:

0.920

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.19

DANN

Benign

0.34

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