dbSNP rs17136953: UMAD1:c.82+62431A>G (chr7-7735884-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001302348.2(UMAD1):c.82+62431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,210 control chromosomes in the GnomAD database, including 7,761 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 0.30 ( 7759 hom., cov: 32)

Exomes 𝑓: 0.39 ( 2 hom. )

Consequence

UMAD1
NM_001302348.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.443

Variant links:

Genes affected

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

UMAD1 links:

ENSG00000270314 (HGNC:):

ENSG00000270314 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2 link	c.82+62431A>G	intron_variant	Intron 2 of 3	ENST00000682710.1	NP_001289277.1	C9J7I0
UMAD1	NM_001302349.2 link	c.82+62431A>G	intron_variant	Intron 2 of 3		NP_001289278.1	C9J7I0
UMAD1	NM_001302350.2 link	c.-24+59676A>G	intron_variant	Intron 3 of 4		NP_001289279.1
LOC100533631		n.7735884A>G	intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1 link	c.82+62431A>G		intron_variant	Intron 2 of 3		NM_001302348.2	ENSP00000507605.1		C9J7I0

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

45163

AN:

152074

Hom.:

7741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.482

Gnomad AMI

AF:

0.446

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.199

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.290

GnomAD4 exome

AF:

0.389

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.125

Gnomad4 NFE exome

AF:

0.600

GnomAD4 genome

AF:

0.297

AC:

45221

AN:

152192

Hom.:

7759

Cov.:

AF XY:

0.293

AC XY:

21775

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.482

Gnomad4 AMR

AF:

0.208

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.273

Gnomad4 FIN

AF:

0.199

Gnomad4 NFE

AF:

0.228

Gnomad4 OTH

AF:

0.291

Alfa

AF:

0.258

Hom.:

750

Bravo

AF:

0.307

Asia WGS

AF:

0.313

AC:

1087

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

DANN

Benign

0.60

Splicing

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