rs1451319

Variant names:

• chr11-58184102-C-T
• rs1451319

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 0.513 in 53,390 control chromosomes in the GnomAD database, including 2,687 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 0.51 (2687 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.539 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: 0.513 AC: 27350 AN: 53308 Hom.: 2684 Cov.: 30

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.575

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.513 AC: 27390 AN: 53390 Hom.: 2687 Cov.: 30 AF XY: 0.515 AC XY: 13769 AN XY: 26720

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.525

Alfa AF: 0.149 Hom.: 1131

Bravo AF: 0.184

Asia WGS AF: 0.167 AC: 554 AN: 3338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1451319; hg19: chr11-57951574;