rs220110

Variant names:

• chr21-42102540-C-A
• rs220110
• ENST00000329015.2:n.1735G>T

Your query was ambiguous. Multiple possible variants found:

• chr21-42102540-C-A
• chr21-42102540-C-G
• chr21-42102540-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000329015.2(UMODL1-AS1):​n.1735G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 237,836 control chromosomes in the GnomAD database, including 11,097 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 0.31 (7187 hom., cov: 32)
  • Exomes 𝑓: 0.30 (3910 hom.)
• Consequence: UMODL1-AS1 ENST00000329015.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 10 publications found

Genes affected

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

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000329015.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMODL1	NM_001004416.3	MANE Select	c.1299+262C>A		intron	N/A	NP_001004416.3
	UMODL1-AS1	NR_027243.1		n.1735G>T		non_coding_transcript_exon	Exon 2 of 2
	UMODL1	NM_173568.4		c.1299+262C>A		intron	N/A	NP_775839.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMODL1-AS1	ENST00000329015.2	TSL:1	n.1735G>T		non_coding_transcript_exon	Exon 2 of 2
	UMODL1	ENST00000408910.7	TSL:1 MANE Select	c.1299+262C>A		intron	N/A	ENSP00000386147.2
	UMODL1	ENST00000408989.6	TSL:1	c.1299+262C>A		intron	N/A	ENSP00000386126.2

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46713 AN: 151986 Hom.: 7181 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.324

GnomAD4 exome AF: 0.302 AC: 25877 AN: 85732 Hom.: 3910 Cov.: 0 AF XY: 0.300 AC XY: 13173 AN XY: 43868

African (AFR) AF: 0.268 AC: 854 AN: 3182

American (AMR) AF: 0.362 AC: 1088 AN: 3002

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1127 AN: 3584

East Asian (EAS) AF: 0.395 AC: 2794 AN: 7082

South Asian (SAS) AF: 0.245 AC: 757 AN: 3096

European-Finnish (FIN) AF: 0.275 AC: 1282 AN: 4660

Middle Eastern (MID) AF: 0.316 AC: 143 AN: 452

European-Non Finnish (NFE) AF: 0.294 AC: 16083 AN: 54670

Other (OTH) AF: 0.291 AC: 1749 AN: 6004

GnomAD4 genome AF: 0.307 AC: 46757 AN: 152104 Hom.: 7187 Cov.: 32 AF XY: 0.305 AC XY: 22686 AN XY: 74354

African (AFR) AF: 0.276 AC: 11424 AN: 41452

American (AMR) AF: 0.342 AC: 5220 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3468

East Asian (EAS) AF: 0.365 AC: 1890 AN: 5182

South Asian (SAS) AF: 0.292 AC: 1410 AN: 4824

European-Finnish (FIN) AF: 0.306 AC: 3234 AN: 10580

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21406 AN: 68006

Other (OTH) AF: 0.326 AC: 688 AN: 2108

Alfa AF: 0.317 Hom.: 10317

Bravo AF: 0.311

Asia WGS AF: 0.326 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.35
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs220110; hg19: chr21-43522650;