11-121431937-A-G

Variant names:

• chr11-121431937-A-G
• rs17125333

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 0.241 in 152,120 control chromosomes in the GnomAD database, including 4,899 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (4899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 11-121431937-A-G is Benign according to our data. Variant chr11-121431937-A-G is described in ClinVar as [Benign]. Clinvar id is 873295.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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: 0.240 AC: 36542 AN: 152002 Hom.: 4875 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.241 AC: 36616 AN: 152120 Hom.: 4899 Cov.: 32 AF XY: 0.237 AC XY: 17591 AN XY: 74360

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.234

Alfa AF: 0.204 Hom.: 2016

Bravo AF: 0.257

Asia WGS AF: 0.182 AC: 632 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	-0.87
CADD	Benign	0.88
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17125333; hg19: chr11-121302646;