rs592190

Variant names:

• chr11-119084604-G-A
• rs592190

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: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.649

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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;