18-57180074-T-G

Position:

• chr18-57180074-T-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 0.37 in 152,042 control chromosomes in the GnomAD database, including 11,435 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 0.37 (11435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56118 AN: 151924 Hom.: 11404 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.370 AC: 56197 AN: 152042 Hom.: 11435 Cov.: 32 AF XY: 0.371 AC XY: 27549 AN XY: 74320

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.316

Alfa AF: 0.256 Hom.: 1235

Bravo AF: 0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12605509; hg19: chr18-54847305;