rs592190

Variant names:

• chr11-119084604-G-A
• rs592190

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.155 AC: 6453 AN: 41516

American (AMR) AF: 0.306 AC: 4657 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3470

East Asian (EAS) AF: 0.745 AC: 3851 AN: 5170

South Asian (SAS) AF: 0.507 AC: 2447 AN: 4830

European-Finnish (FIN) AF: 0.533 AC: 5626 AN: 10558

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.430 AC: 29245 AN: 67954

Other (OTH) AF: 0.367 AC: 776 AN: 2112

Alfa AF: 0.372 Hom.: 1395

Bravo AF: 0.334

Asia WGS AF: 0.586 AC: 2039 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.82
PhyloP100		0.65
PromoterAI		-0.016	Neutral

Splicing

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

Other links and lift over

dbSNP: rs592190; hg19: chr11-118955314;