11-1643386-C-A

Position:

• chr11-1643386-C-A

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 0.776 in 151,896 control chromosomes in the GnomAD database, including 45,880 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 0.78 (45880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117815 AN: 151778 Hom.: 45852 Cov.: 31

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.776 AC: 117892 AN: 151896 Hom.: 45880 Cov.: 31 AF XY: 0.780 AC XY: 57913 AN XY: 74252

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.772

Alfa AF: 0.787 Hom.: 9510

Bravo AF: 0.769

Asia WGS AF: 0.843 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	5.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs902215; hg19: chr11-1664616;