chr18-58043776-A-G

Variant names:

• chr18-58043776-A-G
• rs75982813

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0912 AC: 3784 AN: 41498

American (AMR) AF: 0.0412 AC: 630 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5162

South Asian (SAS) AF: 0.0368 AC: 177 AN: 4804

European-Finnish (FIN) AF: 0.0564 AC: 598 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4173 AN: 67994

Other (OTH) AF: 0.0592 AC: 125 AN: 2110

Alfa AF: 0.0619 Hom.: 464

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
PhyloP100		0.50
PromoterAI		-0.042	Neutral

Splicing

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

Other links and lift over

dbSNP: rs75982813; hg19: chr18-55711008;