rs3846106

Variant names:

• chr3-10293687-C-T
• rs3846106
• ENST00000662597.1:n.1770C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662597.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GHRLOS	NR_004431.3		n.*238C>T		downstream_gene	N/A
	GHRLOS	NR_024144.2		n.*238C>T		downstream_gene	N/A
	GHRLOS	NR_024145.2		n.*238C>T		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GHRLOS	ENST00000662597.1		n.1770C>T		non_coding_transcript_exon	Exon 2 of 2
	SEC13	ENST00000492602.5	TSL:3	n.188-351G>A		intron	N/A
	GHRLOS	ENST00000439539.3	TSL:1	n.*238C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 5399 AN: 152138 Hom.: 215 Cov.: 32

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

African (AFR) AF: 0.0998 AC: 4145 AN: 41530

American (AMR) AF: 0.0156 AC: 238 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.0272 AC: 141 AN: 5188

South Asian (SAS) AF: 0.0516 AC: 249 AN: 4830

European-Finnish (FIN) AF: 0.00160 AC: 17 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00779 AC: 530 AN: 68016

Other (OTH) AF: 0.0255 AC: 54 AN: 2114

Alfa AF: 0.0243 Hom.: 49

Bravo AF: 0.0391

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs3846106; hg19: chr3-10335371;