rs686624

chr11-119084799-T-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.834 in 612,592 control chromosomes in the GnomAD database, including 214,187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.83 (52913 hom., cov: 33)
  • Exomes 𝑓: 0.83 (161274 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.630

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 11-119084799-T-A is Benign according to our data. Variant chr11-119084799-T-A is described in ClinVar as [Benign]. Clinvar id is 255484.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126450 AN: 152112 Hom.: 52879 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.837

GnomAD4 exome AF: 0.835 AC: 384304 AN: 460362 Hom.: 161274 AF XY: 0.837 AC XY: 204931 AN XY: 244712

Gnomad4 AFR exome AF: 0.864

Gnomad4 AMR exome AF: 0.613

Gnomad4 ASJ exome AF: 0.837

Gnomad4 EAS exome AF: 0.926

Gnomad4 SAS exome AF: 0.869

Gnomad4 FIN exome AF: 0.815

Gnomad4 NFE exome AF: 0.837

Gnomad4 OTH exome AF: 0.830

GnomAD4 genome AF: 0.831 AC: 126535 AN: 152230 Hom.: 52913 Cov.: 33 AF XY: 0.829 AC XY: 61708 AN XY: 74428

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.839

Alfa AF: 0.827 Hom.: 6508

Bravo AF: 0.819

Asia WGS AF: 0.900 AC: 3129 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.6
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs686624; hg19: chr11-118955509;