4-189520874-A-G

Variant names:

• chr4-189520874-A-G
• rs1451213

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 0.767 in 152,024 control chromosomes in the GnomAD database, including 45,151 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 0.77 (45151 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.808 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: 0.767 AC: 116544 AN: 151906 Hom.: 45099 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.767 AC: 116661 AN: 152024 Hom.: 45151 Cov.: 31 AF XY: 0.765 AC XY: 56862 AN XY: 74306

African (AFR) AF: 0.794 AC: 32938 AN: 41466

American (AMR) AF: 0.820 AC: 12525 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2903 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2156 AN: 5118

South Asian (SAS) AF: 0.810 AC: 3903 AN: 4820

European-Finnish (FIN) AF: 0.710 AC: 7510 AN: 10580

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52193 AN: 67974

Other (OTH) AF: 0.765 AC: 1619 AN: 2116

Alfa AF: 0.768 Hom.: 5808

Bravo AF: 0.771

Asia WGS AF: 0.680 AC: 2365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.31
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1451213; hg19: chr4-190442028;