18-3031069-A-G

Position:

• chr18-3031069-A-G

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 0.575 in 151,880 control chromosomes in the GnomAD database, including 27,141 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 0.58 (27141 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.3031069A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87280 AN: 151762 Hom.: 27094 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.575 AC: 87382 AN: 151880 Hom.: 27141 Cov.: 31 AF XY: 0.571 AC XY: 42385 AN XY: 74208

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.529

Alfa AF: 0.496 Hom.: 30624

Bravo AF: 0.579

Asia WGS AF: 0.395 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7232826; hg19: chr18-3031067;