3-10284066-T-G

Variant names:

• chr3-10284066-T-G
• rs171336
• ENST00000437082.5:n.*224-1682T>G

Variant summary

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

The ENST00000437082.5(ENSG00000272410):​n.*224-1682T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,116 control chromosomes in the GnomAD database, including 45,083 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 0.76 (45083 hom., cov: 32)
• Consequence: ENSG00000272410 ENST00000437082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 11 publications found

Genes affected

ENSG00000272410 (HGNC:):

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437082.5. 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.52-1682T>G		intron	N/A
	GHRLOS	NR_024144.2		n.134+463T>G		intron	N/A
	GHRLOS	NR_024145.2		n.291+463T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272410	ENST00000437082.5	TSL:2	n.*224-1682T>G		intron	N/A	ENSP00000402783.1
	ENSG00000272410	ENST00000450534.1	TSL:2	n.*2447-1682T>G		intron	N/A	ENSP00000399689.1

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115016 AN: 151998 Hom.: 45031 Cov.: 32

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.731

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.757 AC: 115125 AN: 152116 Hom.: 45083 Cov.: 32 AF XY: 0.762 AC XY: 56659 AN XY: 74362

African (AFR) AF: 0.938 AC: 38947 AN: 41536

American (AMR) AF: 0.796 AC: 12156 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2338 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5139 AN: 5172

South Asian (SAS) AF: 0.902 AC: 4342 AN: 4816

European-Finnish (FIN) AF: 0.622 AC: 6569 AN: 10556

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43248 AN: 67964

Other (OTH) AF: 0.729 AC: 1542 AN: 2116

Alfa AF: 0.738 Hom.: 34048

Bravo AF: 0.775

Asia WGS AF: 0.926 AC: 3220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.54

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

Other links and lift over

dbSNP: rs171336; hg19: chr3-10325750;