rs16872208

Positions:

• chr7-7950856-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110018.1(GLCCI1-DT):​n.465-147A>T variant causes a intron, non coding transcript 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: GLCCI1-DT NR_110018.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

Genes affected

GLCCI1-DT (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GLCCI1-DT	NR_110018.1	n.465-147A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMAD1	ENST00000482067.3	c.157-16843T>A		intron_variant		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

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.0226

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.106

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16872208; hg19: chr7-7990487;