rs220271

chr21-42070144-C-T

Variant summary

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

The ENST00000400427.5(UMODL1):c.-140-5861C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,090 control chromosomes in the GnomAD database, including 44,933 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 0.76 (44933 hom., cov: 33)
• Consequence: UMODL1 ENST00000400427.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UMODL1	NM_001199527.3	c.-140-5861C>T		intron_variant
UMODL1	NM_001199528.4	c.-140-5861C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMODL1	ENST00000400424.6	c.-140-5861C>T		intron_variant		1		A2
UMODL1	ENST00000400427.5	c.-140-5861C>T		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116146 AN: 151972 Hom.: 44910 Cov.: 33

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.764 AC: 116209 AN: 152090 Hom.: 44933 Cov.: 33 AF XY: 0.759 AC XY: 56451 AN XY: 74350

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.779

Alfa AF: 0.804 Hom.: 65172

Bravo AF: 0.769

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.33
Dann	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs220271; hg19: chr21-43490253;