11-121435753-G-A

Variant names:

• chr11-121435753-G-A
• rs4146874

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 0.233 in 151,974 control chromosomes in the GnomAD database, including 4,555 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.23 (4555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 11-121435753-G-A is Benign according to our data. Variant chr11-121435753-G-A is described in ClinVar as [Benign]. Clinvar id is 873293.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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: 0.233 AC: 35407 AN: 151856 Hom.: 4532 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.233 AC: 35477 AN: 151974 Hom.: 4555 Cov.: 32 AF XY: 0.229 AC XY: 17038 AN XY: 74260

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.231

Alfa AF: 0.202 Hom.: 3197

Bravo AF: 0.249

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	-0.89
CADD	Benign	0.19
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4146874; hg19: chr11-121306462;