rs592190

Positions:

• chr11-119084604-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.361 in 152,044 control chromosomes in the GnomAD database, including 11,600 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.36 (11600 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.649

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 11-119084604-G-A is Benign according to our data. Variant chr11-119084604-G-A is described in ClinVar as [Benign]. Clinvar id is 1168307.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.119084604G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54922 AN: 151926 Hom.: 11599 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.361 AC: 54936 AN: 152044 Hom.: 11600 Cov.: 33 AF XY: 0.368 AC XY: 27355 AN XY: 74300

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.367

Alfa AF: 0.372 Hom.: 1395

Bravo AF: 0.334

Asia WGS AF: 0.586 AC: 2039 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs592190; hg19: chr11-118955314;