11-115017879-C-G

Variant names:

• chr11-115017879-C-G
• rs56950471

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 0.284 in 151,818 control chromosomes in the GnomAD database, including 6,317 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 0.28 (6317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43045 AN: 151698 Hom.: 6311 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.284 AC: 43070 AN: 151818 Hom.: 6317 Cov.: 32 AF XY: 0.281 AC XY: 20817 AN XY: 74190

African (AFR) AF: 0.246 AC: 10207 AN: 41434

American (AMR) AF: 0.295 AC: 4490 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3466

East Asian (EAS) AF: 0.148 AC: 765 AN: 5166

South Asian (SAS) AF: 0.354 AC: 1705 AN: 4814

European-Finnish (FIN) AF: 0.293 AC: 3089 AN: 10550

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20911 AN: 67840

Other (OTH) AF: 0.276 AC: 580 AN: 2102

Alfa AF: 0.157 Hom.: 324

Bravo AF: 0.281

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.35
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs56950471; hg19: chr11-114888599;