3-10284066-T-G

Position:

• chr3-10284066-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000272410 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GHRLOS	NR_004431.3	n.52-1682T>G		intron_variant
GHRLOS	NR_024144.2	n.134+463T>G		intron_variant
GHRLOS	NR_024145.2	n.291+463T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000272410	ENST00000437082.5	n.*224-1682T>G		intron_variant		2		ENSP00000402783.1
ENSG00000272410	ENST00000450534.1	n.*2447-1682T>G		intron_variant		2		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

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.729

Alfa AF: 0.687 Hom.: 9241

Bravo AF: 0.775

Asia WGS AF: 0.926 AC: 3220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs171336; hg19: chr3-10325750;