chr18-53771373-G-A

Variant names:

• chr18-53771373-G-A
• rs8087095

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 0.24 in 151,884 control chromosomes in the GnomAD database, including 4,803 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 0.24 (4803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36351 AN: 151766 Hom.: 4792 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.240 AC: 36413 AN: 151884 Hom.: 4803 Cov.: 32 AF XY: 0.237 AC XY: 17586 AN XY: 74250

African (AFR) AF: 0.339 AC: 14060 AN: 41452

American (AMR) AF: 0.169 AC: 2569 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3462

East Asian (EAS) AF: 0.0238 AC: 123 AN: 5176

South Asian (SAS) AF: 0.166 AC: 801 AN: 4824

European-Finnish (FIN) AF: 0.200 AC: 2117 AN: 10560

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15595 AN: 67852

Other (OTH) AF: 0.219 AC: 462 AN: 2108

Alfa AF: 0.245 Hom.: 836

Bravo AF: 0.241

Asia WGS AF: 0.117 AC: 405 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs8087095; hg19: chr18-51297743;