Genetic Variant UMAD1:c.82+14017G>T (chr7-7687470-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001302348.2(UMAD1):c.82+14017G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,056 control chromosomes in the GnomAD database, including 25,282 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 0.57 ( 25270 hom., cov: 31)

Exomes 𝑓: 0.61 ( 12 hom. )

Consequence

UMAD1
NM_001302348.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.634

Publications

7 publications found

Variant links:

Genes affected

UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)

UMAD1 links:

RPA3 (HGNC:10291): (replication protein A3) Enables damaged DNA binding activity and single-stranded DNA binding activity. Involved in DNA repair and DNA replication. Part of DNA replication factor A complex. [provided by Alliance of Genome Resources, Apr 2022]

RPA3 links:

ENSG00000283549 (HGNC:):

ENSG00000283549 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001302348.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
UMAD1	NM_001302348.2	MANE Select	c.82+14017G>T	intron	N/A	NP_001289277.1
RPA3	NM_002947.5	MANE Select	c.-1027-142C>A	intron	N/A	NP_002938.1
UMAD1	NM_001302349.2		c.82+14017G>T	intron	N/A	NP_001289278.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
UMAD1	ENST00000682710.1	MANE Select	c.82+14017G>T	intron	N/A	ENSP00000507605.1
RPA3	ENST00000223129.8	TSL:1 MANE Select	c.-1027-142C>A	intron	N/A	ENSP00000223129.4
UMAD1	ENST00000636849.1	TSL:5	c.82+14017G>T	intron	N/A	ENSP00000489648.1

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87178

AN:

151882

Hom.:

25256

Cov.:

show subpopulations

Gnomad AFR

AF:

0.522

Gnomad AMI

AF:

0.386

Gnomad AMR

AF:

0.623

Gnomad ASJ

AF:

0.579

Gnomad EAS

AF:

0.800

Gnomad SAS

AF:

0.587

Gnomad FIN

AF:

0.599

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.576

Gnomad OTH

AF:

0.546

GnomAD4 exome

AF:

0.607

AC:

AN:

Hom.:

AF XY:

0.568

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.560

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.545

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.574

AC:

87225

AN:

152000

Hom.:

25270

Cov.:

AF XY:

0.577

AC XY:

42849

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.522

AC:

21642

AN:

41448

American (AMR)

AF:

0.624

AC:

9513

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.579

AC:

2008

AN:

3470

East Asian (EAS)

AF:

0.800

AC:

4134

AN:

5168

South Asian (SAS)

AF:

0.586

AC:

2823

AN:

4816

European-Finnish (FIN)

AF:

0.599

AC:

6339

AN:

10578

Middle Eastern (MID)

AF:

0.507

AC:

148

AN:

292

European-Non Finnish (NFE)

AF:

0.576

AC:

39116

AN:

67952

Other (OTH)

AF:

0.546

AC:

1150

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1893

3785

5678

7570

9463

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

744

1488

2232

2976

3720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.557

Hom.:

10130

Bravo

AF:

0.577

Asia WGS

AF:

0.630

AC:

2193

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

4.2

(source)

DANN

Benign

0.79

PhyloP100

0.63

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over