rs4867029

Variant names:

• chr5-30174461-A-G
• rs4867029

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 0.225 in 152,128 control chromosomes in the GnomAD database, including 4,796 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 0.23 (4796 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34249 AN: 152010 Hom.: 4800 Cov.: 33

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.225 AC: 34244 AN: 152128 Hom.: 4796 Cov.: 33 AF XY: 0.222 AC XY: 16483 AN XY: 74344

African (AFR) AF: 0.0822 AC: 3416 AN: 41546

American (AMR) AF: 0.213 AC: 3252 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1017 AN: 3466

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5180

South Asian (SAS) AF: 0.182 AC: 879 AN: 4830

European-Finnish (FIN) AF: 0.320 AC: 3379 AN: 10554

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21297 AN: 67968

Other (OTH) AF: 0.244 AC: 514 AN: 2108

Alfa AF: 0.259 Hom.: 773

Bravo AF: 0.211

Asia WGS AF: 0.0950 AC: 329 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs4867029; hg19: chr5-30174568;