11-27315798-T-G

Variant names:

• chr11-27315798-T-G
• rs1478684

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 0.264 in 152,058 control chromosomes in the GnomAD database, including 5,676 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 0.26 (5676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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: 0.264 AC: 40094 AN: 151940 Hom.: 5667 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.264 AC: 40130 AN: 152058 Hom.: 5676 Cov.: 33 AF XY: 0.269 AC XY: 19976 AN XY: 74318

African (AFR) AF: 0.256 AC: 10609 AN: 41498

American (AMR) AF: 0.388 AC: 5917 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 838 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2371 AN: 5172

South Asian (SAS) AF: 0.429 AC: 2058 AN: 4800

European-Finnish (FIN) AF: 0.196 AC: 2074 AN: 10574

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15553 AN: 67974

Other (OTH) AF: 0.261 AC: 550 AN: 2106

Alfa AF: 0.249 Hom.: 2559

Bravo AF: 0.279

Asia WGS AF: 0.423 AC: 1462 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.91
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1478684; hg19: chr11-27337345;