chr7-7858084-A-C

Variant names:

• chr7-7858084-A-C
• rs2348763
• NM_001302348.2:c.157-19197A>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.157-19197A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,138 control chromosomes in the GnomAD database, including 5,795 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 0.25 (5795 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 10 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.157-19197A>C		intron_variant	Intron 3 of 3	ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.157-19197A>C		intron_variant	Intron 3 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.52-19197A>C		intron_variant	Intron 4 of 4		NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.157-19197A>C		intron_variant	Intron 3 of 3		NM_001302348.2	ENSP00000507605.1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38113 AN: 152020 Hom.: 5797 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.250 AC: 38107 AN: 152138 Hom.: 5795 Cov.: 32 AF XY: 0.249 AC XY: 18510 AN XY: 74370

African (AFR) AF: 0.0762 AC: 3168 AN: 41560

American (AMR) AF: 0.284 AC: 4334 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1003 AN: 5176

South Asian (SAS) AF: 0.310 AC: 1492 AN: 4818

European-Finnish (FIN) AF: 0.283 AC: 2985 AN: 10562

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22648 AN: 67964

Other (OTH) AF: 0.276 AC: 583 AN: 2110

Alfa AF: 0.314 Hom.: 4112

Bravo AF: 0.243

Asia WGS AF: 0.237 AC: 824 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.8
DANN	Benign	0.74
PhyloP100		0.34
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: rs2348763; hg19: chr7-7897715;