18-52238646-A-G

Variant names:

• chr18-52238646-A-G
• rs724349

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 0.147 in 151,966 control chromosomes in the GnomAD database, including 1,835 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 0.15 (1835 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22339 AN: 151848 Hom.: 1832 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.147 AC: 22346 AN: 151966 Hom.: 1835 Cov.: 31 AF XY: 0.151 AC XY: 11235 AN XY: 74244

African (AFR) AF: 0.212 AC: 8801 AN: 41486

American (AMR) AF: 0.0855 AC: 1303 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3470

East Asian (EAS) AF: 0.167 AC: 858 AN: 5130

South Asian (SAS) AF: 0.171 AC: 823 AN: 4818

European-Finnish (FIN) AF: 0.208 AC: 2204 AN: 10578

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7537 AN: 67926

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.120 Hom.: 3397

Bravo AF: 0.140

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs724349; hg19: chr18-49765016;