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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984361	XR_001748316.2	n.318+51920A>G		intron_variant	Intron 2 of 3
LOC107984361	XR_002957260.2	n.395+41528A>G		intron_variant	Intron 3 of 7
LOC107984361	XR_002957261.2	n.318+51920A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302190	ENST00000784851.1	n.475+51920A>G		intron_variant	Intron 2 of 2
ENSG00000302212	ENST00000785017.1	n.161+7794T>C		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs6592362; hg19: chr11-87125438;