11-121432865-T-G

Variant names:

• chr11-121432865-T-G
• rs12417885

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 0.239 in 151,928 control chromosomes in the GnomAD database, including 4,825 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (4825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 11-121432865-T-G is Benign according to our data. Variant chr11-121432865-T-G is described in ClinVar as [Benign]. Clinvar id is 873298.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.238 AC: 36198 AN: 151810 Hom.: 4802 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.239 AC: 36271 AN: 151928 Hom.: 4825 Cov.: 32 AF XY: 0.235 AC XY: 17440 AN XY: 74278

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.233

Alfa AF: 0.223 Hom.: 501

Bravo AF: 0.255

Asia WGS AF: 0.180 AC: 626 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	-0.91
CADD	Benign	0.072
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12417885; hg19: chr11-121303574;