ENST00000828765.1:n.469A>G

Variant names:

• chr17-66301335-T-C
• rs3764402
• ENST00000828765.1:n.469A>G

Variant summary

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

The ENST00000828765.1(ENSG00000307784):​n.469A>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 0.157 in 152,172 control chromosomes in the GnomAD database, including 2,489 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 0.16 (2489 hom., cov: 32)
• Consequence: ENSG00000307784 ENST00000828765.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 9 publications found

Genes affected

ENSG00000307784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000828765.1. 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
	ENSG00000307784	ENST00000828765.1		n.469A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000307784	ENST00000828766.1		n.79A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000307784	ENST00000828767.1		n.287A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23930 AN: 152054 Hom.: 2489 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.157 AC: 23928 AN: 152172 Hom.: 2489 Cov.: 32 AF XY: 0.152 AC XY: 11324 AN XY: 74404

African (AFR) AF: 0.0444 AC: 1846 AN: 41548

American (AMR) AF: 0.114 AC: 1741 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3472

East Asian (EAS) AF: 0.111 AC: 577 AN: 5184

South Asian (SAS) AF: 0.0560 AC: 270 AN: 4818

European-Finnish (FIN) AF: 0.194 AC: 2055 AN: 10582

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16295 AN: 67978

Other (OTH) AF: 0.138 AC: 290 AN: 2108

Alfa AF: 0.211 Hom.: 9662

Bravo AF: 0.147

Asia WGS AF: 0.0730 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.51
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs3764402; hg19: chr17-64297453;