11-56128322-A-G

Variant names:

• chr11-56128322-A-G
• rs17610514

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0217

Gnomad4 AMR AF: 0.0487

Gnomad4 ASJ AF: 0.0298

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0556

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0844

Gnomad4 OTH AF: 0.0651

Alfa AF: 0.0431 Hom.: 36

Bravo AF: 0.0529

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17610514; hg19: chr11-55895798;