chr7-7738344-A-G

Variant names:

• chr7-7738344-A-G
• rs17137001
• NM_001302348.2:c.83-63326A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001302348.2(UMAD1):​c.83-63326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 152,268 control chromosomes in the GnomAD database, including 574 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 0.082 (574 hom., cov: 33)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.83-63326A>G		intron_variant	Intron 2 of 3	ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.83-63326A>G		intron_variant	Intron 2 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.-24+62136A>G		intron_variant	Intron 3 of 4		NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.83-63326A>G		intron_variant	Intron 2 of 3		NM_001302348.2	ENSP00000507605.1

Frequencies

GnomAD3 genomes AF: 0.0817 AC: 12432 AN: 152150 Hom.: 572 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0818 AC: 12458 AN: 152268 Hom.: 574 Cov.: 33 AF XY: 0.0826 AC XY: 6150 AN XY: 74460

African (AFR) AF: 0.127 AC: 5269 AN: 41556

American (AMR) AF: 0.0502 AC: 768 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3472

East Asian (EAS) AF: 0.0146 AC: 76 AN: 5194

South Asian (SAS) AF: 0.115 AC: 557 AN: 4832

European-Finnish (FIN) AF: 0.0690 AC: 731 AN: 10594

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0644 AC: 4379 AN: 68008

Other (OTH) AF: 0.0757 AC: 160 AN: 2114

Alfa AF: 0.0692 Hom.: 508

Bravo AF: 0.0817

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.87
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17137001; hg19: chr7-7777975;