Genetic Variant ENSG00000284823:n.722-41775A>G (chr6-4623578-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 ENST00000716074.1(ENSG00000284823):n.722-41775A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 152,184 control chromosomes in the GnomAD database, including 1,360 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 0.079 ( 1360 hom., cov: 32)

Consequence

ENSG00000284823
ENST00000716074.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360

Publications

0 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000284823	ENST00000716074.1 link	n.722-41775A>G	intron_variant	Intron 3 of 4
ENSG00000284823	ENST00000827010.1 link	n.243+23973A>G	intron_variant	Intron 1 of 2
ENSG00000284823	ENST00000827011.1 link	n.220+23973A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0783

AC:

11903

AN:

152066

Hom.:

1354

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0347

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.0345

Gnomad SAS

AF:

0.0431

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00360

Gnomad OTH

AF:

0.0613

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

GnomAD4 genome

AF:

0.0786

AC:

11956

AN:

152184

Hom.:

1360

Cov.:

AF XY:

0.0780

AC XY:

5802

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.255

AC:

10589

AN:

41470

American (AMR)

AF:

0.0346

AC:

530

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.0164

AC:

AN:

3466

East Asian (EAS)

AF:

0.0346

AC:

179

AN:

5178

South Asian (SAS)

AF:

0.0444

AC:

214

AN:

4824

European-Finnish (FIN)

AF:

0.000283

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00360

AC:

245

AN:

68004

Other (OTH)

AF:

0.0635

AC:

134

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

453

906

1359

1812

2265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0439

Hom.:

212

Bravo

AF:

0.0874

Asia WGS

AF:

0.0760

AC:

263

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

2.8

(source)

DANN

Benign

0.35

PhyloP100

0.036

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