11-121432865-T-G

Position:

• chr11-121432865-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 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 (no stars).

• Frequency: Genomes: 𝑓 0.24 (4825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -13 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 no_assertion_criteria_provided, 0 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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: no assertion criteria provided

Submissions by phenotype

not specified Benign:1

Benign, no assertion criteria provided

case-control

Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University

Apr 02, 2020

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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;