rs4264496

Variant names:

• chr18-22608274-C-T
• rs4264496

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 0.452 in 152,064 control chromosomes in the GnomAD database, including 15,914 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 0.45 (15914 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.612 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: 0.452 AC: 68656 AN: 151946 Hom.: 15911 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.452 AC: 68685 AN: 152064 Hom.: 15914 Cov.: 33 AF XY: 0.456 AC XY: 33871 AN XY: 74336

African (AFR) AF: 0.403 AC: 16700 AN: 41472

American (AMR) AF: 0.622 AC: 9511 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1520 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2596 AN: 5172

South Asian (SAS) AF: 0.484 AC: 2332 AN: 4822

European-Finnish (FIN) AF: 0.405 AC: 4276 AN: 10564

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30294 AN: 67964

Other (OTH) AF: 0.463 AC: 975 AN: 2106

Alfa AF: 0.467 Hom.: 9958

Bravo AF: 0.466

Asia WGS AF: 0.526 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.2
DANN	Benign	0.67
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs4264496; hg19: chr18-20188237;