chr18-60262199-G-A

Variant names:

• chr18-60262199-G-A
• rs17700633

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 0.278 in 152,048 control chromosomes in the GnomAD database, including 6,160 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 0.28 (6160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 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: 0.278 AC: 42205 AN: 151930 Hom.: 6157 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.278 AC: 42235 AN: 152048 Hom.: 6160 Cov.: 32 AF XY: 0.270 AC XY: 20093 AN XY: 74312

African (AFR) AF: 0.310 AC: 12837 AN: 41450

American (AMR) AF: 0.199 AC: 3037 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3472

East Asian (EAS) AF: 0.0611 AC: 316 AN: 5172

South Asian (SAS) AF: 0.369 AC: 1781 AN: 4822

European-Finnish (FIN) AF: 0.219 AC: 2315 AN: 10592

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20246 AN: 67956

Other (OTH) AF: 0.256 AC: 541 AN: 2114

Alfa AF: 0.291 Hom.: 8919

Bravo AF: 0.274

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.14
DANN	Benign	0.70
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs17700633; hg19: chr18-57929432;