18-57493445-C-T

Variant names:

• chr18-57493445-C-T
• rs4940796

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 0.0835 in 152,262 control chromosomes in the GnomAD database, including 1,031 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 0.083 (1031 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 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: 0.0832 AC: 12664 AN: 152144 Hom.: 1017 Cov.: 34

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0801

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.0835 AC: 12713 AN: 152262 Hom.: 1031 Cov.: 34 AF XY: 0.0886 AC XY: 6593 AN XY: 74446

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.0232

Gnomad4 FIN AF: 0.0801

Gnomad4 NFE AF: 0.0320

Gnomad4 OTH AF: 0.0832

Alfa AF: 0.0780 Hom.: 211

Bravo AF: 0.100

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.58
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4940796; hg19: chr18-55160677;