rs1397048

chr11-56698623-C-T

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 0.53 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 (no stars).

• Frequency: Genomes: 𝑓 0.53 (17767 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -1.67

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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: 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	-0.98
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;