18-56263975-C-T

Position:

• chr18-56263975-C-T

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 0.728 in 151,994 control chromosomes in the GnomAD database, including 40,771 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 0.73 (40771 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110489 AN: 151876 Hom.: 40721 Cov.: 30

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.728 AC: 110600 AN: 151994 Hom.: 40771 Cov.: 30 AF XY: 0.726 AC XY: 53934 AN XY: 74254

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.724

Alfa AF: 0.693 Hom.: 61851

Bravo AF: 0.742

Asia WGS AF: 0.780 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1237238; hg19: chr18-53931206;