chr18-57503042-G-A

Variant names:

• chr18-57503042-G-A
• rs11662635

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 0.0555 in 152,250 control chromosomes in the GnomAD database, including 769 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 0.055 (769 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• 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 (EAS) allele frequency at 95% confidence interval = 0.349 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: 0.0553 AC: 8418 AN: 152130 Hom.: 759 Cov.: 33

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0575

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

GnomAD4 genome AF: 0.0555 AC: 8447 AN: 152250 Hom.: 769 Cov.: 33 AF XY: 0.0618 AC XY: 4598 AN XY: 74442

African (AFR) AF: 0.0121 AC: 502 AN: 41568

American (AMR) AF: 0.184 AC: 2820 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1874 AN: 5170

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4830

European-Finnish (FIN) AF: 0.0831 AC: 880 AN: 10596

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0307 AC: 2090 AN: 68010

Other (OTH) AF: 0.0564 AC: 119 AN: 2110

Alfa AF: 0.0345 Hom.: 130

Bravo AF: 0.0687

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs11662635; hg19: chr18-55170274;