ENST00000766247.1:n.283-6404T>G

Variant names:

• chr6-32427688-T-G
• rs1894552
• ENST00000766247.1:n.283-6404T>G

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.283-6404T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,198 control chromosomes in the GnomAD database, including 1,642 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 0.14 (1642 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 8 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766247.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299769	ENST00000766247.1		n.283-6404T>G		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.391+2216T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20545 AN: 152080 Hom.: 1642 Cov.: 32

Gnomad AFR AF: 0.0658

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0932

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.135 AC: 20552 AN: 152198 Hom.: 1642 Cov.: 32 AF XY: 0.133 AC XY: 9932 AN XY: 74412

African (AFR) AF: 0.0661 AC: 2744 AN: 41536

American (AMR) AF: 0.116 AC: 1775 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3468

East Asian (EAS) AF: 0.126 AC: 656 AN: 5186

South Asian (SAS) AF: 0.0928 AC: 448 AN: 4826

European-Finnish (FIN) AF: 0.205 AC: 2173 AN: 10594

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12001 AN: 67982

Other (OTH) AF: 0.132 AC: 280 AN: 2114

Alfa AF: 0.102 Hom.: 249

Bravo AF: 0.126

Asia WGS AF: 0.127 AC: 439 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.37
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1894552; hg19: chr6-32395465;