chr18-56467257-T-C

Position:

• chr18-56467257-T-C

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 0.183 in 152,176 control chromosomes in the GnomAD database, including 2,962 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 0.18 (2962 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

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 (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.183 AC: 27841 AN: 152058 Hom.: 2958 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.183 AC: 27837 AN: 152176 Hom.: 2962 Cov.: 32 AF XY: 0.186 AC XY: 13815 AN XY: 74394

Gnomad4 AFR AF: 0.0724

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.210

Alfa AF: 0.222 Hom.: 1826

Bravo AF: 0.172

Asia WGS AF: 0.198 AC: 690 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11875674; hg19: chr18-54134488;