11-121431110-C-A

Variant names:

• chr11-121431110-C-A
• rs17125331

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 152,146 control chromosomes in the GnomAD database, including 7,949 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.29 (7949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.99

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 11-121431110-C-A is Benign according to our data. Variant chr11-121431110-C-A is described in ClinVar as [Benign]. Clinvar id is 873290.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: 43409 AN: 152028 Hom.: 7916 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.134

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: 43500 AN: 152146 Hom.: 7949 Cov.: 32 AF XY: 0.279 AC XY: 20761 AN XY: 74364

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.269

Alfa AF: 0.204 Hom.: 5698

Bravo AF: 0.310

Asia WGS AF: 0.193 AC: 673 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	-0.98
CADD	Benign	0.035
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17125331; hg19: chr11-121301819;