3-30305713-T-C

Position:

• chr3-30305713-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.748 in 151,874 control chromosomes in the GnomAD database, including 43,094 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 0.75 (43094 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30305713T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113448 AN: 151756 Hom.: 43044 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.748 AC: 113561 AN: 151874 Hom.: 43094 Cov.: 31 AF XY: 0.751 AC XY: 55755 AN XY: 74218

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.704

Alfa AF: 0.703 Hom.: 18443

Bravo AF: 0.752

Asia WGS AF: 0.816 AC: 2837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1495581; hg19: chr3-30347204;