7-7739693-T-C

Variant names:

• chr7-7739693-T-C
• rs10486187
• NM_001302348.2:c.83-61977T>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.83-61977T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,216 control chromosomes in the GnomAD database, including 1,096 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 0.12 (1096 hom., cov: 33)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 1 publications found

Genes affected

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

ENSG00000293038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 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.83-61977T>C		intron	N/A	NP_001289277.1	C9J7I0
	UMAD1	NM_001302349.2		c.83-61977T>C		intron	N/A	NP_001289278.1	C9J7I0
	UMAD1	NM_001302350.2		c.-23-61977T>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.83-61977T>C		intron	N/A	ENSP00000507605.1	C9J7I0
	UMAD1	ENST00000949980.1		c.190-48964T>C		intron	N/A	ENSP00000620039.1
	UMAD1	ENST00000636849.1	TSL:5	c.83-61977T>C		intron	N/A	ENSP00000489648.1	C9J7I0

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17691 AN: 152098 Hom.: 1099 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0981

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.116 AC: 17696 AN: 152216 Hom.: 1096 Cov.: 33 AF XY: 0.115 AC XY: 8582 AN XY: 74424

African (AFR) AF: 0.158 AC: 6572 AN: 41522

American (AMR) AF: 0.0912 AC: 1395 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3470

East Asian (EAS) AF: 0.125 AC: 650 AN: 5182

South Asian (SAS) AF: 0.123 AC: 592 AN: 4832

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10600

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0981 AC: 6671 AN: 68008

Other (OTH) AF: 0.101 AC: 213 AN: 2108

Alfa AF: 0.0960 Hom.: 1011

Bravo AF: 0.117

Asia WGS AF: 0.143 AC: 497 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10486187; hg19: chr7-7779324;