rs6659742

Variant summary

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

The NR_147123.1(SNHG28):​n.116+6199G>A 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 0.39 in 151,924 control chromosomes in the GnomAD database, including 11,701 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 0.39 ( 11701 hom., cov: 31)

Consequence

SNHG28
NR_147123.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.99
Variant links:
Genes affected
SNHG28 (HGNC:27647): (small nucleolar RNA host gene 28) Enables RNA binding activity. [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=-0.84).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SNHG28NR_147123.1 linkuse as main transcriptn.116+6199G>A intron_variant, non_coding_transcript_variant
SNHG28NR_147122.1 linkuse as main transcriptn.281+6034G>A intron_variant, non_coding_transcript_variant
SNHG28NR_147124.1 linkuse as main transcriptn.281+6034G>A intron_variant, non_coding_transcript_variant
SNHG28NR_147125.1 linkuse as main transcriptn.281+6034G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SNHG28ENST00000676072.1 linkuse as main transcriptn.150+6199G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.390
AC:
59247
AN:
151806
Hom.:
11686
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.369
Gnomad AMI
AF:
0.351
Gnomad AMR
AF:
0.458
Gnomad ASJ
AF:
0.399
Gnomad EAS
AF:
0.264
Gnomad SAS
AF:
0.375
Gnomad FIN
AF:
0.379
Gnomad MID
AF:
0.329
Gnomad NFE
AF:
0.401
Gnomad OTH
AF:
0.379
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.390
AC:
59295
AN:
151924
Hom.:
11701
Cov.:
31
AF XY:
0.391
AC XY:
29044
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.369
Gnomad4 AMR
AF:
0.459
Gnomad4 ASJ
AF:
0.399
Gnomad4 EAS
AF:
0.264
Gnomad4 SAS
AF:
0.374
Gnomad4 FIN
AF:
0.379
Gnomad4 NFE
AF:
0.401
Gnomad4 OTH
AF:
0.377
Alfa
AF:
0.402
Hom.:
16191
Bravo
AF:
0.395
Asia WGS
AF:
0.346
AC:
1202
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
13
DANN
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs6659742; hg19: chr1-159818513; API