Genetic Variant ENSG00000284823:n.313+68894A>G (chr6-4512745-T-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000642310.1(ENSG00000284823):n.313+68894A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00324 in 149,088 control chromosomes in the GnomAD database, including 3 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 0.0032 ( 3 hom., cov: 31)

Consequence

ENSG00000284823
ENST00000642310.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.785

Publications

2 publications found

Variant links:

Genes affected

ENSG00000284823 (HGNC:):

ENSG00000284823 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105374894	XR_001743940.2 link	n.288-45083A>G	intron_variant	Intron 2 of 2
LOC105374894	XR_007059417.1 link	n.288-48766A>G	intron_variant	Intron 2 of 2
LOC105374894	XR_007059418.1 link	n.287+68894A>G	intron_variant	Intron 2 of 3
LOC105374894	XR_926409.3 link	n.288-14419A>G	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000284823	ENST00000642310.1 link	n.313+68894A>G	intron_variant	Intron 2 of 4
ENSG00000284823	ENST00000716074.1 link	n.887-45083A>G	intron_variant	Intron 4 of 4
ENSG00000284823	ENST00000827010.1 link	n.409-45083A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.00323

AC:

481

AN:

149040

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0112

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00113

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000446

Gnomad OTH

AF:

0.00387

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

GnomAD4 genome

AF:

0.00324

AC:

483

AN:

149088

Hom.:

Cov.:

AF XY:

0.00311

AC XY:

226

AN XY:

72588

show subpopulations

African (AFR)

AF:

0.0113

AC:

455

AN:

40416

American (AMR)

AF:

0.00113

AC:

AN:

15044

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3442

East Asian (EAS)

AF:

0.00

AC:

AN:

5056

South Asian (SAS)

AF:

0.00

AC:

AN:

4628

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9942

Middle Eastern (MID)

AF:

0.00

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.0000446

AC:

AN:

67286

Other (OTH)

AF:

0.00384

AC:

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

100

125

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00217

Hom.:

Bravo

AF:

0.00362

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.45

(source)

DANN

Benign

0.58

PhyloP100

-0.79

Splicing

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

Publications

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6-4512745-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