chr18-56267556-A-G

Position:

• chr18-56267556-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 0.785 in 152,030 control chromosomes in the GnomAD database, including 47,482 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 0.79 (47482 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• 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.56267556A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119225 AN: 151912 Hom.: 47421 Cov.: 31

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.785 AC: 119350 AN: 152030 Hom.: 47482 Cov.: 31 AF XY: 0.783 AC XY: 58198 AN XY: 74286

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.779

Alfa AF: 0.744 Hom.: 10194

Bravo AF: 0.799

Asia WGS AF: 0.797 AC: 2772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	2.0
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: rs1229598; hg19: chr18-53934787;