rs6979457

Variant names:

• chr7-7870237-A-C
• rs6979457
• NM_001302348.2:c.157-7044A>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.157-7044A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,004 control chromosomes in the GnomAD database, including 35,159 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 0.68 (35159 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 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.157-7044A>C		intron	N/A	NP_001289277.1	C9J7I0
	UMAD1	NM_001302349.2		c.157-7044A>C		intron	N/A	NP_001289278.1	C9J7I0
	UMAD1	NM_001302350.2		c.52-7044A>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.157-7044A>C		intron	N/A	ENSP00000507605.1	C9J7I0
	UMAD1	ENST00000949980.1		c.358-7044A>C		intron	N/A	ENSP00000620039.1
	UMAD1	ENST00000636849.1	TSL:5	c.157-7044A>C		intron	N/A	ENSP00000489648.1	C9J7I0

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103074 AN: 151886 Hom.: 35112 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.679 AC: 103171 AN: 152004 Hom.: 35159 Cov.: 32 AF XY: 0.678 AC XY: 50399 AN XY: 74284

African (AFR) AF: 0.723 AC: 29965 AN: 41468

American (AMR) AF: 0.693 AC: 10592 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2031 AN: 3464

East Asian (EAS) AF: 0.506 AC: 2612 AN: 5160

South Asian (SAS) AF: 0.663 AC: 3195 AN: 4820

European-Finnish (FIN) AF: 0.688 AC: 7241 AN: 10532

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45264 AN: 67978

Other (OTH) AF: 0.665 AC: 1401 AN: 2108

Alfa AF: 0.683 Hom.: 5515

Bravo AF: 0.680

Asia WGS AF: 0.589 AC: 2038 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		-0.0090
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: rs6979457; hg19: chr7-7909868;