7-7967878-T-C

Variant names:

• chr7-7967878-T-C
• rs37972
• ENST00000482067.3:c.*105T>C

Variant summary

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

The ENST00000482067.3(UMAD1):​c.*105T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 396,838 control chromosomes in the GnomAD database, including 73,941 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 0.63 (31349 hom., cov: 32)
  • Exomes 𝑓: 0.59 (42592 hom.)
• Consequence: UMAD1 ENST00000482067.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 54 publications found

Genes affected

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

GLCCI1-DT (HGNC:40852): (GLCCI1 divergent transcript)

ENSG00000283549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLCCI1-DT	NR_110018.1	n.209+666A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000482067.3	c.*105T>C		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000490046.1
GLCCI1-DT	ENST00000428660.1	n.132+1894A>G		intron_variant	Intron 1 of 1	4
GLCCI1-DT	ENST00000451066.2	n.56+666A>G		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96474 AN: 151966 Hom.: 31315 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.658

GnomAD4 exome AF: 0.587 AC: 143755 AN: 244754 Hom.: 42592 Cov.: 0 AF XY: 0.585 AC XY: 72565 AN XY: 123988

African (AFR) AF: 0.789 AC: 5640 AN: 7148

American (AMR) AF: 0.571 AC: 4226 AN: 7396

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 5842 AN: 9200

East Asian (EAS) AF: 0.581 AC: 13247 AN: 22790

South Asian (SAS) AF: 0.472 AC: 1245 AN: 2636

European-Finnish (FIN) AF: 0.576 AC: 11887 AN: 20650

Middle Eastern (MID) AF: 0.649 AC: 838 AN: 1292

European-Non Finnish (NFE) AF: 0.577 AC: 90820 AN: 157368

Other (OTH) AF: 0.615 AC: 10010 AN: 16274

GnomAD4 genome AF: 0.635 AC: 96551 AN: 152084 Hom.: 31349 Cov.: 32 AF XY: 0.631 AC XY: 46916 AN XY: 74352

African (AFR) AF: 0.789 AC: 32733 AN: 41494

American (AMR) AF: 0.601 AC: 9185 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2234 AN: 3472

East Asian (EAS) AF: 0.569 AC: 2945 AN: 5172

South Asian (SAS) AF: 0.473 AC: 2284 AN: 4824

European-Finnish (FIN) AF: 0.583 AC: 6150 AN: 10556

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39000 AN: 67974

Other (OTH) AF: 0.653 AC: 1376 AN: 2108

Alfa AF: 0.591 Hom.: 105468

Bravo AF: 0.648

Asia WGS AF: 0.510 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.65
DANN	Benign	0.29
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs37972; hg19: chr7-8007509;