ENST00000766247.1:n.282+6562T>C

Variant names:

• chr6-32420932-T-C
• rs3135366
• ENST00000766247.1:n.282+6562T>C

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.282+6562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,136 control chromosomes in the GnomAD database, including 1,537 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 0.13 (1537 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 27 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299769	ENST00000766247.1		n.282+6562T>C		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.287-4436T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19782 AN: 152018 Hom.: 1537 Cov.: 32

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.130 AC: 19788 AN: 152136 Hom.: 1537 Cov.: 32 AF XY: 0.127 AC XY: 9446 AN XY: 74350

African (AFR) AF: 0.0767 AC: 3183 AN: 41506

American (AMR) AF: 0.112 AC: 1717 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0888 AC: 308 AN: 3470

East Asian (EAS) AF: 0.0389 AC: 201 AN: 5172

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4826

European-Finnish (FIN) AF: 0.205 AC: 2168 AN: 10580

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11621 AN: 67974

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.149 Hom.: 2192

Bravo AF: 0.122

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.48
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs3135366; hg19: chr6-32388709;