Genetic Variant GHRLOS:n.1544T>C (chr3-10293461-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000662597.1(GHRLOS):n.1544T>C 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 0.316 in 152,118 control chromosomes in the GnomAD database, including 8,267 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 0.32 ( 8266 hom., cov: 32)

Exomes 𝑓: 0.38 ( 1 hom. )

Consequence

GHRLOS
ENST00000662597.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.271

Publications

18 publications found

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]

GHRLOS links:

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]

SEC13 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
GHRLOS	NR_004431.3 link	n.*12T>C	downstream_gene_variant
GHRLOS	NR_024144.2 link	n.*12T>C	downstream_gene_variant
GHRLOS	NR_024145.2 link	n.*12T>C	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GHRLOS	ENST00000662597.1 link	n.1544T>C	non_coding_transcript_exon_variant	Exon 2 of 2
SEC13	ENST00000492602.5 link	n.188-125A>G	intron_variant	Intron 2 of 2	3
GHRLOS	ENST00000439539.3 link	n.*12T>C	downstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

48018

AN:

151984

Hom.:

8256

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.549

Gnomad SAS

AF:

0.472

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.303

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.167

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.316

AC:

48071

AN:

152102

Hom.:

8266

Cov.:

AF XY:

0.326

AC XY:

24258

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.274

AC:

11381

AN:

41510

American (AMR)

AF:

0.440

AC:

6720

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

894

AN:

3468

East Asian (EAS)

AF:

0.548

AC:

2835

AN:

5170

South Asian (SAS)

AF:

0.470

AC:

2260

AN:

4808

European-Finnish (FIN)

AF:

0.370

AC:

3905

AN:

10560

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.280

AC:

19059

AN:

67982

Other (OTH)

AF:

0.304

AC:

643

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1665

3331

4996

6662

8327

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.293

Hom.:

11770

Bravo

AF:

0.320

Asia WGS

AF:

0.502

AC:

1741

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

4.3

(source)

DANN

Benign

0.70

PhyloP100

-0.27

Mutation Taster

=99/1

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over