20-58834449-C-T

Variant summary

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

The ENST00000601795.1(ENSG00000268333):​n.513G>A 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 0.417 in 149,144 control chromosomes in the GnomAD database, including 14,230 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 0.42 ( 14207 hom., cov: 31)
Exomes 𝑓: 0.71 ( 23 hom. )

Consequence

ENSG00000268333
ENST00000601795.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36
Variant links:
Genes affected
GNAS-AS1 (HGNC:24872): (GNAS antisense RNA 1) This gene produces a paternally-imprinted antisense RNA transcript that helps regulate the GNAS complex locus, which encodes the alpha subunit of the stimulatory G protein. Defects in this gene are a cause of pseudohypoparathyroidism type Ib.[provided by RefSeq, Jun 2010]

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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GNAS-AS1NR_190185.1 linkn.892G>A non_coding_transcript_exon_variant Exon 5 of 5
GNAS-AS1NR_002785.3 linkn.818+7488G>A intron_variant Intron 4 of 4
GNAS-AS1NR_185847.1 linkn.672+7488G>A intron_variant Intron 4 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GNAS-AS1ENST00000424094.6 linkn.819+7488G>A intron_variant Intron 4 of 4 1
ENSG00000268333ENST00000601795.1 linkn.513G>A non_coding_transcript_exon_variant Exon 2 of 2 3
GNAS-AS1ENST00000443966.2 linkn.2120+4276G>A intron_variant Intron 1 of 1 5

Frequencies

GnomAD3 genomes
AF:
0.417
AC:
62086
AN:
148938
Hom.:
14213
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.232
Gnomad AMI
AF:
0.531
Gnomad AMR
AF:
0.474
Gnomad ASJ
AF:
0.369
Gnomad EAS
AF:
0.794
Gnomad SAS
AF:
0.494
Gnomad FIN
AF:
0.543
Gnomad MID
AF:
0.338
Gnomad NFE
AF:
0.461
Gnomad OTH
AF:
0.412
GnomAD4 exome
AF:
0.714
AC:
60
AN:
84
Hom.:
23
Cov.:
0
AF XY:
0.697
AC XY:
46
AN XY:
66
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 EAS exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.681
Gnomad4 OTH exome
AF:
1.00
GnomAD4 genome
AF:
0.417
AC:
62091
AN:
149060
Hom.:
14207
Cov.:
31
AF XY:
0.423
AC XY:
30775
AN XY:
72832
show subpopulations
Gnomad4 AFR
AF:
0.232
Gnomad4 AMR
AF:
0.474
Gnomad4 ASJ
AF:
0.369
Gnomad4 EAS
AF:
0.794
Gnomad4 SAS
AF:
0.492
Gnomad4 FIN
AF:
0.543
Gnomad4 NFE
AF:
0.461
Gnomad4 OTH
AF:
0.407
Alfa
AF:
0.403
Hom.:
1943
Bravo
AF:
0.401
Asia WGS
AF:
0.551
AC:
1914
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.12
DANN
Benign
0.58

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: rs6026549; hg19: chr20-57409504; API