rs16872208

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0440
Variant links:
Genes affected
UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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-DTNR_110018.1 linkuse as main transcriptn.465-147A>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UMAD1ENST00000482067.3 linkuse as main transcriptc.157-16843T>A intron_variant 5

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16872208; hg19: chr7-7990487; API