18-56261410-A-G

Position:

• chr18-56261410-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 0.784 in 152,098 control chromosomes in the GnomAD database, including 47,351 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 0.78 (47351 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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 (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56261410A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119067 AN: 151980 Hom.: 47290 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.784 AC: 119192 AN: 152098 Hom.: 47351 Cov.: 32 AF XY: 0.782 AC XY: 58114 AN XY: 74334

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.777

Alfa AF: 0.746 Hom.: 8714

Bravo AF: 0.798

Asia WGS AF: 0.797 AC: 2771 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	0.80
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2538026; hg19: chr18-53928641;