18-67346654-C-T

Variant names:

• chr18-67346654-C-T
• rs12969428

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 0.0995 in 152,102 control chromosomes in the GnomAD database, including 991 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 0.099 (991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 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: 0.0995 AC: 15128 AN: 151990 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0995 AC: 15133 AN: 152102 Hom.: 991 Cov.: 32 AF XY: 0.105 AC XY: 7814 AN XY: 74344

African (AFR) AF: 0.0458 AC: 1902 AN: 41502

American (AMR) AF: 0.0991 AC: 1513 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1633 AN: 5136

South Asian (SAS) AF: 0.113 AC: 545 AN: 4822

European-Finnish (FIN) AF: 0.204 AC: 2162 AN: 10582

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0959 AC: 6518 AN: 68000

Other (OTH) AF: 0.113 AC: 239 AN: 2112

Alfa AF: 0.0955 Hom.: 2486

Bravo AF: 0.0934

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.39
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs12969428; hg19: chr18-65013891;