chr11-102843985-C-G

Position:

• chr11-102843985-C-G

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 0.576 in 152,022 control chromosomes in the GnomAD database, including 25,795 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.58 (25795 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 11-102843985-C-G is Benign according to our data. Variant chr11-102843985-C-G is described in ClinVar as [Benign]. Clinvar id is 1222602.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102843985C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87516 AN: 151904 Hom.: 25757 Cov.: 33

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.576 AC: 87612 AN: 152022 Hom.: 25795 Cov.: 33 AF XY: 0.585 AC XY: 43454 AN XY: 74278

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.561

Alfa AF: 0.397 Hom.: 1149

Bravo AF: 0.581

Asia WGS AF: 0.665 AC: 2313 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

This variant is associated with the following publications: (PMID: 12915441, 18810583) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.096
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs617819; hg19: chr11-102714716;