11-6321099-T-G

Variant names:

• chr11-6321099-T-G
• rs1488864
• ENST00000833456.1:n.597T>G

Variant summary

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

The ENST00000833456.1(ENSG00000282556):​n.597T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,212 control chromosomes in the GnomAD database, including 50,799 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 0.80 (50799 hom., cov: 33)
• Consequence: ENSG00000282556 ENST00000833456.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 15 publications found

Genes affected

ENSG00000282556 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833456.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282556	ENST00000833456.1		n.597T>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000282556	ENST00000649129.2		n.558+1402T>G		intron	N/A
	ENSG00000282556	ENST00000652923.1		n.164+1402T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121881 AN: 152094 Hom.: 50795 Cov.: 33

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.801 AC: 121933 AN: 152212 Hom.: 50799 Cov.: 33 AF XY: 0.801 AC XY: 59598 AN XY: 74412

African (AFR) AF: 0.547 AC: 22703 AN: 41496

American (AMR) AF: 0.896 AC: 13717 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2889 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4730 AN: 5164

South Asian (SAS) AF: 0.786 AC: 3798 AN: 4830

European-Finnish (FIN) AF: 0.908 AC: 9628 AN: 10600

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61689 AN: 68026

Other (OTH) AF: 0.818 AC: 1728 AN: 2112

Alfa AF: 0.874 Hom.: 107577

Bravo AF: 0.789

Asia WGS AF: 0.808 AC: 2813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1488864; hg19: chr11-6342329;