NM_001302348.2:c.157-33589A>C

Variant names:

• chr7-7843692-A-C
• rs7780564
• NM_001302348.2:c.157-33589A>C

Variant summary

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

The NM_001302348.2(UMAD1):​c.157-33589A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,336 control chromosomes in the GnomAD database, including 21,915 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 0.54 (21915 hom., cov: 31)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 9 publications found

Genes affected

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

ENSG00000283549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.576 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	NM_001302348.2	MANE Select	c.157-33589A>C		intron	N/A	NP_001289277.1	C9J7I0
	UMAD1	NM_001302349.2		c.157-33589A>C		intron	N/A	NP_001289278.1	C9J7I0
	UMAD1	NM_001302350.2		c.52-33589A>C		intron	N/A	NP_001289279.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	ENST00000682710.1	MANE Select	c.157-33589A>C		intron	N/A	ENSP00000507605.1	C9J7I0
	UMAD1	ENST00000949980.1		c.358-33589A>C		intron	N/A	ENSP00000620039.1
	UMAD1	ENST00000636849.1	TSL:5	c.157-33589A>C		intron	N/A	ENSP00000489648.1	C9J7I0

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81029 AN: 151216 Hom.: 21915 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.536 AC: 81055 AN: 151336 Hom.: 21915 Cov.: 31 AF XY: 0.533 AC XY: 39365 AN XY: 73924

African (AFR) AF: 0.531 AC: 21895 AN: 41206

American (AMR) AF: 0.462 AC: 7034 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2238 AN: 3462

East Asian (EAS) AF: 0.428 AC: 2204 AN: 5148

South Asian (SAS) AF: 0.594 AC: 2854 AN: 4806

European-Finnish (FIN) AF: 0.540 AC: 5648 AN: 10450

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.550 AC: 37252 AN: 67726

Other (OTH) AF: 0.562 AC: 1183 AN: 2106

Alfa AF: 0.548 Hom.: 63633

Bravo AF: 0.531

Asia WGS AF: 0.501 AC: 1743 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7780564; hg19: chr7-7883323;