rs75982813

Positions:

• chr18-58043776-A-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 0.0634 in 152,130 control chromosomes in the GnomAD database, including 336 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 0.063 (336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0888 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: 0.0634 AC: 9645 AN: 152012 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0415

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0370

Gnomad FIN AF: 0.0564

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0599

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

GnomAD4 genome AF: 0.0634 AC: 9642 AN: 152130 Hom.: 336 Cov.: 32 AF XY: 0.0616 AC XY: 4585 AN XY: 74380

Gnomad4 AFR AF: 0.0912

Gnomad4 AMR AF: 0.0412

Gnomad4 ASJ AF: 0.0366

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0368

Gnomad4 FIN AF: 0.0564

Gnomad4 NFE AF: 0.0614

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0629 Hom.: 85

Bravo AF: 0.0639

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	12
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75982813; hg19: chr18-55711008;