Genetic Variant ENSG00000303463:n.393-11556C>G (chr1-60405454-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000794751.1(ENSG00000303463):n.393-11556C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,124 control chromosomes in the GnomAD database, including 1,110 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 0.11 ( 1110 hom., cov: 32)

Consequence

ENSG00000303463
ENST00000794751.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.553

Publications

1 publications found

Variant links:

Genes affected

ENSG00000303463 (HGNC:):

ENSG00000303463 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303463	ENST00000794751.1 link	n.393-11556C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

17093

AN:

152006

Hom.:

1109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0704

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.0970

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0458

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.105

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

GnomAD4 genome

AF:

0.112

AC:

17096

AN:

152124

Hom.:

1110

Cov.:

AF XY:

0.111

AC XY:

8249

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.0704

AC:

2920

AN:

41494

American (AMR)

AF:

0.0969

AC:

1481

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

397

AN:

3466

East Asian (EAS)

AF:

0.00135

AC:

AN:

5174

South Asian (SAS)

AF:

0.0460

AC:

222

AN:

4822

European-Finnish (FIN)

AF:

0.155

AC:

1635

AN:

10582

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.147

AC:

9994

AN:

67986

Other (OTH)

AF:

0.104

AC:

220

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

783

1565

2348

3130

3913

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.0553

Hom.:

Bravo

AF:

0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.3

(source)

DANN

Benign

0.35

PhyloP100

-0.55

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