18-56261410-A-G

Variant names:

• chr18-56261410-A-G
• rs2538026

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;