3-10293687-C-T

Variant summary

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

The ENST00000662597.1(GHRLOS):​n.1770C>T 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 0.0355 in 152,256 control chromosomes in the GnomAD database, including 214 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 0.036 ( 214 hom., cov: 32)

Consequence

GHRLOS
ENST00000662597.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.925
Variant links:
Genes affected
GHRLOS (HGNC:33885): (ghrelin opposite strand/antisense RNA) This gene is an antisense gene of the ghrelin/obestatin prepropeptide gene. Alternatively spliced transcript variants have been identified and they may function as non-coding regulatory RNAs. [provided by RefSeq, Jan 2013]
SEC13 (HGNC:10697): (SEC13 homolog, nuclear pore and COPII coat complex component) The protein encoded by this gene belongs to the SEC13 family of WD-repeat proteins. It is a constituent of the endoplasmic reticulum and the nuclear pore complex. It has similarity to the yeast SEC13 protein, which is required for vesicle biogenesis from endoplasmic reticulum during the transport of proteins. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0973 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GHRLOSENST00000662597.1 linkn.1770C>T non_coding_transcript_exon_variant 2/2
SEC13ENST00000492602.5 linkn.188-351G>A intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0355
AC:
5399
AN:
152138
Hom.:
215
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0998
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0156
Gnomad ASJ
AF:
0.00749
Gnomad EAS
AF:
0.0271
Gnomad SAS
AF:
0.0519
Gnomad FIN
AF:
0.00160
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00779
Gnomad OTH
AF:
0.0258
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0355
AC:
5406
AN:
152256
Hom.:
214
Cov.:
32
AF XY:
0.0352
AC XY:
2623
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0998
Gnomad4 AMR
AF:
0.0156
Gnomad4 ASJ
AF:
0.00749
Gnomad4 EAS
AF:
0.0272
Gnomad4 SAS
AF:
0.0516
Gnomad4 FIN
AF:
0.00160
Gnomad4 NFE
AF:
0.00779
Gnomad4 OTH
AF:
0.0255
Alfa
AF:
0.0269
Hom.:
38
Bravo
AF:
0.0391
Asia WGS
AF:
0.0430
AC:
151
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.5
DANN
Benign
0.70

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: rs3846106; hg19: chr3-10335371; API