7-7735884-A-G

Variant names:

• chr7-7735884-A-G
• rs17136953
• NM_001302348.2:c.82+62431A>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.82+62431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,210 control chromosomes in the GnomAD database, including 7,761 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 0.30 (7759 hom., cov: 32)
  • Exomes 𝑓: 0.39 (2 hom.)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 3 publications found

Genes affected

UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)

ENSG00000270314 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	NM_001302348.2	MANE Select	c.82+62431A>G		intron	N/A	NP_001289277.1
	UMAD1	NM_001302349.2		c.82+62431A>G		intron	N/A	NP_001289278.1
	UMAD1	NM_001302350.2		c.-24+59676A>G		intron	N/A	NP_001289279.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	ENST00000682710.1	MANE Select	c.82+62431A>G		intron	N/A	ENSP00000507605.1
	ENSG00000270314	ENST00000604734.1	TSL:6	n.968T>C		non_coding_transcript_exon	Exon 1 of 1
	UMAD1	ENST00000636849.1	TSL:5	c.82+62431A>G		intron	N/A	ENSP00000489648.1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45163 AN: 152074 Hom.: 7741 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.389 AC: 7 AN: 18 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 5 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.600 AC: 6 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.297 AC: 45221 AN: 152192 Hom.: 7759 Cov.: 32 AF XY: 0.293 AC XY: 21775 AN XY: 74414

African (AFR) AF: 0.482 AC: 20019 AN: 41496

American (AMR) AF: 0.208 AC: 3173 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1152 AN: 5194

South Asian (SAS) AF: 0.273 AC: 1320 AN: 4832

European-Finnish (FIN) AF: 0.199 AC: 2105 AN: 10576

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15513 AN: 68012

Other (OTH) AF: 0.291 AC: 616 AN: 2116

Alfa AF: 0.258 Hom.: 750

Bravo AF: 0.307

Asia WGS AF: 0.313 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.60
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs17136953; hg19: chr7-7775515;