rs5019445

Variant names:

• chr4-181204969-A-G
• rs5019445

Your query was ambiguous. Multiple possible variants found:

• chr4-181204969-A-G
• chr4-181204969-A-T

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 0.731 in 151,826 control chromosomes in the GnomAD database, including 40,954 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 0.73 (40954 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 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: 0.731 AC: 110976 AN: 151714 Hom.: 40921 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.731 AC: 111052 AN: 151826 Hom.: 40954 Cov.: 31 AF XY: 0.739 AC XY: 54809 AN XY: 74192

African (AFR) AF: 0.699 AC: 28928 AN: 41358

American (AMR) AF: 0.730 AC: 11122 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2359 AN: 3470

East Asian (EAS) AF: 0.965 AC: 4973 AN: 5152

South Asian (SAS) AF: 0.878 AC: 4229 AN: 4818

European-Finnish (FIN) AF: 0.828 AC: 8711 AN: 10518

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.714 AC: 48518 AN: 67976

Other (OTH) AF: 0.700 AC: 1475 AN: 2106

Alfa AF: 0.715 Hom.: 151392

Bravo AF: 0.718

Asia WGS AF: 0.911 AC: 3165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.46
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs5019445; hg19: chr4-182126122;