rs1451319

Variant names:

• chr11-58184102-C-T
• rs1451319

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 0.513 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.513 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

African (AFR) AF: 0.479 AC: 9185 AN: 19194

American (AMR) AF: 0.555 AC: 3260 AN: 5878

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 769 AN: 1410

East Asian (EAS) AF: 0.539 AC: 1074 AN: 1994

South Asian (SAS) AF: 0.530 AC: 482 AN: 910

European-Finnish (FIN) AF: 0.561 AC: 2475 AN: 4412

Middle Eastern (MID) AF: 0.563 AC: 71 AN: 126

European-Non Finnish (NFE) AF: 0.517 AC: 9531 AN: 18430

Other (OTH) AF: 0.525 AC: 424 AN: 808

Alfa AF: 0.156 Hom.: 1675

Bravo AF: 0.184

Asia WGS AF: 0.167 AC: 554 AN: 3338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.91
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1451319; hg19: chr11-57951574;