18-57180074-T-G

Variant names:

• chr18-57180074-T-G
• rs12605509

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;