rs17664267

Variant names:

• chr18-43228833-G-T
• rs17664267

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 0.165 in 152,004 control chromosomes in the GnomAD database, including 2,325 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 0.16 (2325 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.165 AC: 24995 AN: 151886 Hom.: 2321 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.0962

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.165 AC: 25017 AN: 152004 Hom.: 2325 Cov.: 32 AF XY: 0.164 AC XY: 12194 AN XY: 74322

African (AFR) AF: 0.102 AC: 4247 AN: 41462

American (AMR) AF: 0.170 AC: 2600 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3468

East Asian (EAS) AF: 0.00541 AC: 28 AN: 5174

South Asian (SAS) AF: 0.111 AC: 533 AN: 4820

European-Finnish (FIN) AF: 0.239 AC: 2517 AN: 10548

Middle Eastern (MID) AF: 0.0931 AC: 27 AN: 290

European-Non Finnish (NFE) AF: 0.204 AC: 13879 AN: 67960

Other (OTH) AF: 0.164 AC: 345 AN: 2108

Alfa AF: 0.181 Hom.: 6119

Bravo AF: 0.158

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs17664267; hg19: chr18-40808798;