chr7-7808456-C-T

Variant names:

• chr7-7808456-C-T
• rs10237037
• NM_001302348.2:c.156+6713C>T

Variant summary

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

The NM_001302348.2(UMAD1):​c.156+6713C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0423 in 151,988 control chromosomes in the GnomAD database, including 210 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 0.042 (210 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 3 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0923 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.156+6713C>T		intron	N/A	NP_001289277.1
	UMAD1	NM_001302349.2		c.156+6713C>T		intron	N/A	NP_001289278.1
	UMAD1	NM_001302350.2		c.51+6713C>T		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.156+6713C>T		intron	N/A	ENSP00000507605.1
	UMAD1	ENST00000949980.1		c.357+6713C>T		intron	N/A	ENSP00000620039.1
	UMAD1	ENST00000636849.1	TSL:5	c.156+6713C>T		intron	N/A	ENSP00000489648.1

Frequencies

GnomAD3 genomes AF: 0.0423 AC: 6428 AN: 151870 Hom.: 210 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.00878

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0423

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

GnomAD4 genome AF: 0.0423 AC: 6433 AN: 151988 Hom.: 210 Cov.: 32 AF XY: 0.0416 AC XY: 3094 AN XY: 74290

African (AFR) AF: 0.0948 AC: 3933 AN: 41486

American (AMR) AF: 0.0335 AC: 511 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0210 AC: 73 AN: 3472

East Asian (EAS) AF: 0.0426 AC: 221 AN: 5186

South Asian (SAS) AF: 0.0444 AC: 214 AN: 4824

European-Finnish (FIN) AF: 0.00878 AC: 93 AN: 10590

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0182 AC: 1232 AN: 67858

Other (OTH) AF: 0.0419 AC: 88 AN: 2100

Alfa AF: 0.0281 Hom.: 176

Bravo AF: 0.0464

Asia WGS AF: 0.0550 AC: 192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.2
DANN	Benign	0.72
PhyloP100		0.055
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: rs10237037; hg19: chr7-7848087;