11-56128322-A-G

Variant names:

• chr11-56128322-A-G
• rs17610514

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 0.0598 in 151,748 control chromosomes in the GnomAD database, including 372 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 0.060 (372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0825 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: 0.0598 AC: 9071 AN: 151630 Hom.: 372 Cov.: 32

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0298

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0554

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.0657

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

GnomAD4 genome AF: 0.0598 AC: 9076 AN: 151748 Hom.: 372 Cov.: 32 AF XY: 0.0594 AC XY: 4404 AN XY: 74168

African (AFR) AF: 0.0217 AC: 899 AN: 41484

American (AMR) AF: 0.0487 AC: 739 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.0298 AC: 103 AN: 3460

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0556 AC: 268 AN: 4818

European-Finnish (FIN) AF: 0.109 AC: 1150 AN: 10562

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0844 AC: 5717 AN: 67772

Other (OTH) AF: 0.0651 AC: 137 AN: 2106

Alfa AF: 0.0525 Hom.: 97

Bravo AF: 0.0529

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs17610514; hg19: chr11-55895798;