chr7-7825120-A-G

Variant names:

• chr7-7825120-A-G
• rs12702661
• NM_001302348.2:c.156+23377A>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.156+23377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 151,984 control chromosomes in the GnomAD database, including 47,725 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 0.79 (47725 hom., cov: 30)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.156+23377A>G		intron_variant	Intron 3 of 3	ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.156+23377A>G		intron_variant	Intron 3 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.51+23377A>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.156+23377A>G		intron_variant	Intron 3 of 3		NM_001302348.2	ENSP00000507605.1

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120261 AN: 151866 Hom.: 47690 Cov.: 30

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.792 AC: 120349 AN: 151984 Hom.: 47725 Cov.: 30 AF XY: 0.794 AC XY: 59001 AN XY: 74266

African (AFR) AF: 0.837 AC: 34715 AN: 41462

American (AMR) AF: 0.749 AC: 11420 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2660 AN: 3470

East Asian (EAS) AF: 0.761 AC: 3914 AN: 5144

South Asian (SAS) AF: 0.808 AC: 3891 AN: 4816

European-Finnish (FIN) AF: 0.815 AC: 8635 AN: 10596

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.774 AC: 52565 AN: 67946

Other (OTH) AF: 0.761 AC: 1604 AN: 2108

Alfa AF: 0.776 Hom.: 197463

Bravo AF: 0.787

Asia WGS AF: 0.783 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		0.11
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: rs12702661; hg19: chr7-7864751;