rs4862188

Variant names:

• chr4-183434217-C-T
• rs4862188

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 0.57 in 149,844 control chromosomes in the GnomAD database, including 27,897 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 0.57 (27897 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 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: 0.570 AC: 85364 AN: 149726 Hom.: 27879 Cov.: 29

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.570 AC: 85406 AN: 149844 Hom.: 27897 Cov.: 29 AF XY: 0.564 AC XY: 41287 AN XY: 73258

African (AFR) AF: 0.258 AC: 10637 AN: 41168

American (AMR) AF: 0.535 AC: 8078 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1948 AN: 3430

East Asian (EAS) AF: 0.399 AC: 2042 AN: 5112

South Asian (SAS) AF: 0.463 AC: 2204 AN: 4764

European-Finnish (FIN) AF: 0.743 AC: 7723 AN: 10398

Middle Eastern (MID) AF: 0.524 AC: 152 AN: 290

European-Non Finnish (NFE) AF: 0.763 AC: 50818 AN: 66630

Other (OTH) AF: 0.585 AC: 1215 AN: 2078

Alfa AF: 0.654 Hom.: 3905

Bravo AF: 0.545

Asia WGS AF: 0.448 AC: 1557 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.32
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs4862188; hg19: chr4-184355370;