chr15-55823327-A-G

Variant names:

• chr15-55823327-A-G
• rs11071224

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 0.0808 in 152,246 control chromosomes in the GnomAD database, including 693 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 0.081 (693 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 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: 0.0807 AC: 12277 AN: 152128 Hom.: 692 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0826

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0808 AC: 12300 AN: 152246 Hom.: 693 Cov.: 32 AF XY: 0.0822 AC XY: 6118 AN XY: 74438

African (AFR) AF: 0.142 AC: 5879 AN: 41530

American (AMR) AF: 0.0549 AC: 840 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3470

East Asian (EAS) AF: 0.172 AC: 892 AN: 5176

South Asian (SAS) AF: 0.0826 AC: 399 AN: 4828

European-Finnish (FIN) AF: 0.0761 AC: 808 AN: 10612

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0439 AC: 2985 AN: 68018

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

Alfa AF: 0.0559 Hom.: 962

Bravo AF: 0.0811

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.67
DANN	Benign	0.25
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11071224; hg19: chr15-56115525;