11-56453599-G-C

Variant names:

• chr11-56453599-G-C
• rs615231

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 0.169 in 152,082 control chromosomes in the GnomAD database, including 2,645 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 0.17 (2645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 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: 0.170 AC: 25766 AN: 151964 Hom.: 2646 Cov.: 32

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.169 AC: 25761 AN: 152082 Hom.: 2645 Cov.: 32 AF XY: 0.168 AC XY: 12486 AN XY: 74322

African (AFR) AF: 0.0498 AC: 2070 AN: 41532

American (AMR) AF: 0.152 AC: 2317 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3466

East Asian (EAS) AF: 0.132 AC: 682 AN: 5154

South Asian (SAS) AF: 0.169 AC: 815 AN: 4824

European-Finnish (FIN) AF: 0.212 AC: 2251 AN: 10598

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15949 AN: 67940

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.124 Hom.: 237

Bravo AF: 0.159

Asia WGS AF: 0.128 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.51
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs615231; hg19: chr11-56221075;