chr11-56698623-C-T

Variant names:

• chr11-56698623-C-T
• rs1397048

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 0.53 in 134,264 control chromosomes in the GnomAD database, including 17,767 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.53 (17767 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.67

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 11-56698623-C-T is Benign according to our data. Variant chr11-56698623-C-T is described in ClinVar as [Benign]. Clinvar id is 873251.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 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: 0.530 AC: 71053 AN: 134154 Hom.: 17727 Cov.: 35

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.486

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.530 AC: 71131 AN: 134264 Hom.: 17767 Cov.: 35 AF XY: 0.526 AC XY: 34394 AN XY: 65430

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.486

Alfa AF: 0.401 Hom.: 24603

Asia WGS AF: 0.288 AC: 1000 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	0.053
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1397048; hg19: chr11-56466099; COSMIC: COSV56450500;