chr18-57508517-G-A

Position:

• chr18-57508517-G-A

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 0.593 in 152,078 control chromosomes in the GnomAD database, including 27,577 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 0.59 (27577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 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: 0.594 AC: 90198 AN: 151960 Hom.: 27578 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.593 AC: 90213 AN: 152078 Hom.: 27577 Cov.: 32 AF XY: 0.578 AC XY: 42994 AN XY: 74328

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.583

Alfa AF: 0.633 Hom.: 14108

Bravo AF: 0.586

Asia WGS AF: 0.391 AC: 1364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
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: rs10503018; hg19: chr18-55175749;