chr18-68625022-T-G

Variant names:

• chr18-68625022-T-G
• rs17232800

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 0.0675 in 152,210 control chromosomes in the GnomAD database, including 390 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 0.067 (390 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 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: 0.0674 AC: 10255 AN: 152090 Hom.: 389 Cov.: 30

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0873

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0733

Gnomad OTH AF: 0.0622

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

GnomAD4 genome AF: 0.0675 AC: 10270 AN: 152210 Hom.: 390 Cov.: 30 AF XY: 0.0685 AC XY: 5100 AN XY: 74418

African (AFR) AF: 0.0431 AC: 1790 AN: 41532

American (AMR) AF: 0.0873 AC: 1336 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0308 AC: 107 AN: 3472

East Asian (EAS) AF: 0.150 AC: 779 AN: 5178

South Asian (SAS) AF: 0.0874 AC: 421 AN: 4816

European-Finnish (FIN) AF: 0.0649 AC: 688 AN: 10600

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0733 AC: 4985 AN: 67998

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0726 Hom.: 286

Bravo AF: 0.0678

Asia WGS AF: 0.109 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs17232800; hg19: chr18-66292259;