rs1451213

Variant names:

• chr4-189520874-A-G
• rs1451213

Your query was ambiguous. Multiple possible variants found:

• chr4-189520874-A-G
• chr4-189520874-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.765

Alfa AF: 0.766 Hom.: 5559

Bravo AF: 0.771

Asia WGS AF: 0.680 AC: 2365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1451213; hg19: chr4-190442028;