rs3846106

Positions:

• chr3-10293687-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

GHRLOS (HGNC:):

ACMG classification

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
		n.10293687C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GHRLOS	ENST00000662597.1	n.1770C>T		non_coding_transcript_exon_variant	2/2
SEC13	ENST00000492602.5	n.188-351G>A		intron_variant		3

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

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

Other links and lift over

dbSNP: rs3846106; hg19: chr3-10335371;