chr3-10293461-T-C

Variant names:

• chr3-10293461-T-C
• rs10490815
• ENST00000662597.1:n.1544T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 18 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 (EAS) allele frequency at 95% confidence interval = 0.532 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.*12T>C		downstream_gene	N/A
	GHRLOS	NR_024144.2		n.*12T>C		downstream_gene	N/A
	GHRLOS	NR_024145.2		n.*12T>C		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GHRLOS	ENST00000662597.1		n.1544T>C		non_coding_transcript_exon	Exon 2 of 2
	SEC13	ENST00000492602.5	TSL:3	n.188-125A>G		intron	N/A
	GHRLOS	ENST00000439539.3	TSL:1	n.*12T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48018 AN: 151984 Hom.: 8256 Cov.: 32

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: 6 AN: 16 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.167 AC: 1 AN: 6

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 4 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.316 AC: 48071 AN: 152102 Hom.: 8266 Cov.: 32 AF XY: 0.326 AC XY: 24258 AN XY: 74358

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: 80 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19059 AN: 67982

Other (OTH) AF: 0.304 AC: 643 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		-0.27
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10490815; hg19: chr3-10335145;