4-54528005-C-T

Variant names:

• chr4-54528005-C-T
• rs218237

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 0.181 in 152,066 control chromosomes in the GnomAD database, including 2,880 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 0.18 (2880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 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: 0.181 AC: 27519 AN: 151948 Hom.: 2873 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.181 AC: 27551 AN: 152066 Hom.: 2880 Cov.: 32 AF XY: 0.186 AC XY: 13812 AN XY: 74338

African (AFR) AF: 0.240 AC: 9940 AN: 41474

American (AMR) AF: 0.226 AC: 3459 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1713 AN: 5144

South Asian (SAS) AF: 0.269 AC: 1295 AN: 4810

European-Finnish (FIN) AF: 0.158 AC: 1675 AN: 10598

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8610 AN: 67984

Other (OTH) AF: 0.173 AC: 363 AN: 2104

Alfa AF: 0.147 Hom.: 8546

Bravo AF: 0.188

Asia WGS AF: 0.292 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.67
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs218237; hg19: chr4-55394172;