Genetic Variant ENSG00000304708:n.339-1464A>G (chr6-69596007-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 ENST00000805732.1(ENSG00000304708):n.339-1464A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,016 control chromosomes in the GnomAD database, including 20,450 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 0.52 ( 20450 hom., cov: 32)

Consequence

ENSG00000304708
ENST00000805732.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449

Publications

2 publications found

Variant links:

Genes affected

ENSG00000304708 (HGNC:):

ENSG00000304708 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000304708	ENST00000805732.1 link	n.339-1464A>G	intron_variant	Intron 2 of 2
ENSG00000304708	ENST00000805733.1 link	n.522-1464A>G	intron_variant	Intron 2 of 2
ENSG00000304708	ENST00000805734.1 link	n.339-1464A>G	intron_variant	Intron 2 of 2
ENSG00000304708	ENST00000805735.1 link	n.96-1464A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

78352

AN:

151900

Hom.:

20425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.574

Gnomad AMI

AF:

0.545

Gnomad AMR

AF:

0.460

Gnomad ASJ

AF:

0.504

Gnomad EAS

AF:

0.624

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.498

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.493

Gnomad OTH

AF:

0.467

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

GnomAD4 genome

AF:

0.516

AC:

78433

AN:

152016

Hom.:

20450

Cov.:

AF XY:

0.515

AC XY:

38320

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.574

AC:

23784

AN:

41436

American (AMR)

AF:

0.461

AC:

7041

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.504

AC:

1748

AN:

3468

East Asian (EAS)

AF:

0.624

AC:

3232

AN:

5176

South Asian (SAS)

AF:

0.469

AC:

2256

AN:

4814

European-Finnish (FIN)

AF:

0.498

AC:

5265

AN:

10576

Middle Eastern (MID)

AF:

0.339

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.493

AC:

33522

AN:

67966

Other (OTH)

AF:

0.470

AC:

990

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1956

3911

5867

7822

9778

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.501

Hom.:

71802

Bravo

AF:

0.519

Asia WGS

AF:

0.538

AC:

1872

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.54

(source)

DANN

Benign

0.38

PhyloP100

-0.45

Splicing

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

Publications

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6-69596007-T-C

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