rs16872208

Variant names:

• chr7-7950856-T-A
• rs16872208
• ENST00000482067.3:c.157-16843T>A

Variant summary

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

The ENST00000482067.3(UMAD1):​c.157-16843T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,262 control chromosomes in the GnomAD database, including 769 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 0.087 (769 hom., cov: 32)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: UMAD1 ENST00000482067.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLCCI1-DT	NR_110018.1	n.465-147A>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000482067.3	c.157-16843T>A		intron_variant	Intron 3 of 3	5		ENSP00000490046.1
GLCCI1-DT	ENST00000451066.2	n.156-147A>T		intron_variant	Intron 2 of 3	5
ENSG00000283549	ENST00000469183.5	n.492-53052T>A		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13255 AN: 152110 Hom.: 769 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.107

GnomAD4 exome AF: 0.118 AC: 4 AN: 34 Hom.: 0 AF XY: 0.125 AC XY: 3 AN XY: 24

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) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.115 AC: 3 AN: 26

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.0871 AC: 13253 AN: 152228 Hom.: 769 Cov.: 32 AF XY: 0.0909 AC XY: 6769 AN XY: 74428

African (AFR) AF: 0.0226 AC: 939 AN: 41556

American (AMR) AF: 0.135 AC: 2062 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3468

East Asian (EAS) AF: 0.130 AC: 673 AN: 5184

South Asian (SAS) AF: 0.103 AC: 497 AN: 4826

European-Finnish (FIN) AF: 0.152 AC: 1612 AN: 10586

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

European-Non Finnish (NFE) AF: 0.100 AC: 6808 AN: 68000

Other (OTH) AF: 0.106 AC: 223 AN: 2110

Alfa AF: 0.0925 Hom.: 77

Bravo AF: 0.0828

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.6
DANN	Benign	0.67
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs16872208; hg19: chr7-7990487;