rs6592362

Variant names:

• chr11-87414396-A-G
• rs6592362
• ENST00000784851.1:n.475+51920A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000784851.1(ENSG00000302190):​n.475+51920A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 152,154 control chromosomes in the GnomAD database, including 36,682 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.69 (36682 hom., cov: 33)
• Consequence: ENSG00000302190 ENST00000784851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 19 publications found

Genes affected

ENSG00000302190 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784851.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302190	ENST00000784851.1		n.475+51920A>G		intron	N/A
	ENSG00000302212	ENST00000785017.1		n.161+7794T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104435 AN: 152036 Hom.: 36649 Cov.: 33

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.687 AC: 104522 AN: 152154 Hom.: 36682 Cov.: 33 AF XY: 0.677 AC XY: 50396 AN XY: 74394

African (AFR) AF: 0.730 AC: 30295 AN: 41506

American (AMR) AF: 0.555 AC: 8477 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2487 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1652 AN: 5188

South Asian (SAS) AF: 0.631 AC: 3045 AN: 4826

European-Finnish (FIN) AF: 0.635 AC: 6713 AN: 10568

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49732 AN: 67990

Other (OTH) AF: 0.673 AC: 1422 AN: 2114

Alfa AF: 0.821 Hom.: 11155

Bravo AF: 0.683

Asia WGS AF: 0.531 AC: 1846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.79

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6592362;

hg19: chr11-87125438;