7-7856822-C-G

Variant names:

• chr7-7856822-C-G
• rs17495770
• NM_001302348.2:c.157-20459C>G

Variant summary

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

The NM_001302348.2(UMAD1):​c.157-20459C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,180 control chromosomes in the GnomAD database, including 1,112 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 0.10 (1112 hom., cov: 33)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.157-20459C>G		intron_variant	Intron 3 of 3	ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.157-20459C>G		intron_variant	Intron 3 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.52-20459C>G		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.157-20459C>G		intron_variant	Intron 3 of 3		NM_001302348.2	ENSP00000507605.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15598 AN: 152062 Hom.: 1113 Cov.: 33

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.102 AC: 15593 AN: 152180 Hom.: 1112 Cov.: 33 AF XY: 0.102 AC XY: 7612 AN XY: 74394

African (AFR) AF: 0.0236 AC: 982 AN: 41538

American (AMR) AF: 0.0908 AC: 1388 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.122 AC: 589 AN: 4828

European-Finnish (FIN) AF: 0.140 AC: 1483 AN: 10564

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10073 AN: 67996

Other (OTH) AF: 0.119 AC: 250 AN: 2108

Alfa AF: 0.131 Hom.: 216

Bravo AF: 0.0943

Asia WGS AF: 0.0500 AC: 175 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.65
PhyloP100		-0.041
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: rs17495770; hg19: chr7-7896453;