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GeneBe

rs28362491

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000563833.1(null):n.319_322del variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 153,546 control chromosomes in the GnomAD database, including 14,272 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 14166 hom., cov: 0)
Exomes 𝑓: 0.32 ( 106 hom. )

Consequence


ENST00000563833.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0720
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105377621NR_136202.1 linkuse as main transcriptn.48+1438_48+1441del intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000563833.1 linkuse as main transcriptn.319_322del non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.428
AC:
64938
AN:
151662
Hom.:
14138
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.494
Gnomad AMI
AF:
0.359
Gnomad AMR
AF:
0.484
Gnomad ASJ
AF:
0.333
Gnomad EAS
AF:
0.402
Gnomad SAS
AF:
0.298
Gnomad FIN
AF:
0.447
Gnomad MID
AF:
0.297
Gnomad NFE
AF:
0.391
Gnomad OTH
AF:
0.402
GnomAD4 exome
AF:
0.323
AC:
570
AN:
1764
Hom.:
106
AF XY:
0.327
AC XY:
353
AN XY:
1080
show subpopulations
Gnomad4 AFR exome
AF:
0.350
Gnomad4 AMR exome
AF:
0.429
Gnomad4 ASJ exome
AF:
0.139
Gnomad4 EAS exome
AF:
0.313
Gnomad4 SAS exome
AF:
0.167
Gnomad4 FIN exome
AF:
0.489
Gnomad4 NFE exome
AF:
0.331
Gnomad4 OTH exome
AF:
0.256
GnomAD4 genome
AF:
0.428
AC:
65010
AN:
151782
Hom.:
14166
Cov.:
0
AF XY:
0.429
AC XY:
31815
AN XY:
74188
show subpopulations
Gnomad4 AFR
AF:
0.494
Gnomad4 AMR
AF:
0.485
Gnomad4 ASJ
AF:
0.333
Gnomad4 EAS
AF:
0.403
Gnomad4 SAS
AF:
0.297
Gnomad4 FIN
AF:
0.447
Gnomad4 NFE
AF:
0.391
Gnomad4 OTH
AF:
0.398
Alfa
AF:
0.416
Hom.:
1645
Bravo
AF:
0.439
Asia WGS
AF:
0.354
AC:
1226
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs28362491; hg19: chr4-103422154; API