11-121432497-G-A

Variant names:

• chr11-121432497-G-A
• rs17125336

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.286 in 151,976 control chromosomes in the GnomAD database, including 7,929 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.29 (7929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.335

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 11-121432497-G-A is Benign according to our data. Variant chr11-121432497-G-A is described in ClinVar as [Benign]. Clinvar id is 873296.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 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: 0.286 AC: 43393 AN: 151858 Hom.: 7896 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.286 AC: 43484 AN: 151976 Hom.: 7929 Cov.: 32 AF XY: 0.279 AC XY: 20757 AN XY: 74310

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.269

Alfa AF: 0.247 Hom.: 1664

Bravo AF: 0.311

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Apr 02, 2020

Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: case-control

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17125336; hg19: chr11-121303206;