rs1209349

Variant summary

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

The ENST00000503433.5(UNC93A):​c.-51-8417G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0331 in 152,154 control chromosomes in the GnomAD database, including 285 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 0.033 ( 285 hom., cov: 32)

Consequence

UNC93A
ENST00000503433.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.238
Variant links:
Genes affected
UNC93A (HGNC:12570): (unc-93 homolog A) Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UNC93AXM_011535905.3 linkuse as main transcriptc.-51-8417G>T intron_variant
UNC93AXM_011535906.3 linkuse as main transcriptc.-52+1861G>T intron_variant
UNC93AXM_011535908.3 linkuse as main transcriptc.-51-8417G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UNC93AENST00000503433.5 linkuse as main transcriptc.-51-8417G>T intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0330
AC:
5024
AN:
152036
Hom.:
285
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.109
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0115
Gnomad ASJ
AF:
0.0237
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00373
Gnomad FIN
AF:
0.000378
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00270
Gnomad OTH
AF:
0.0315
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0331
AC:
5039
AN:
152154
Hom.:
285
Cov.:
32
AF XY:
0.0313
AC XY:
2329
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.109
Gnomad4 AMR
AF:
0.0115
Gnomad4 ASJ
AF:
0.0237
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00373
Gnomad4 FIN
AF:
0.000378
Gnomad4 NFE
AF:
0.00271
Gnomad4 OTH
AF:
0.0312
Alfa
AF:
0.0230
Hom.:
23
Bravo
AF:
0.0379
Asia WGS
AF:
0.00924
AC:
32
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.60
DANN
Benign
0.36

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: rs1209349; hg19: chr6-167696510; API