Genetic Variant ENSG00000307784:n.469A>G (chr17-66301335-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0190

Publications

9 publications found

Variant links:

Genes affected

ENSG00000307784 (HGNC:):

ENSG00000307784 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000307784	ENST00000828765.1 link	n.469A>G	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000307784	ENST00000828766.1 link	n.79A>G	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000307784	ENST00000828767.1 link	n.287A>G	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23930

AN:

152054

Hom.:

2489

Cov.:

show subpopulations

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.:

AF XY:

0.152

AC XY:

11324

AN XY:

74404

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16295

AN:

67978

Other (OTH)

AF:

0.138

AC:

290

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

981

1962

2944

3925

4906

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

258

516

774

1032

1290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.4

(source)

DANN

Benign

0.51

PhyloP100

0.019

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over