rs11158098

Variant names:

• chr14-56429428-C-T
• rs11158098

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 0.233 in 152,180 control chromosomes in the GnomAD database, including 4,695 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 0.23 (4695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 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: 0.233 AC: 35383 AN: 152062 Hom.: 4698 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.233 AC: 35388 AN: 152180 Hom.: 4695 Cov.: 32 AF XY: 0.234 AC XY: 17426 AN XY: 74396

African (AFR) AF: 0.122 AC: 5061 AN: 41550

American (AMR) AF: 0.205 AC: 3134 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1196 AN: 5180

South Asian (SAS) AF: 0.231 AC: 1116 AN: 4830

European-Finnish (FIN) AF: 0.318 AC: 3354 AN: 10562

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19458 AN: 67984

Other (OTH) AF: 0.257 AC: 543 AN: 2110

Alfa AF: 0.269 Hom.: 10075

Bravo AF: 0.220

Asia WGS AF: 0.210 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.64
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs11158098; hg19: chr14-56896146;