Genetic Variant ENSG00000293080:n.769-13659A>G (chr1-119448806-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 ENST00000632456.2(ENSG00000293080):n.769-13659A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,148 control chromosomes in the GnomAD database, including 2,208 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 0.14 ( 2208 hom., cov: 33)

Consequence

ENSG00000293080
ENST00000632456.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

Publications

4 publications found

Variant links:

Genes affected

ENSG00000293080 (HGNC:):

ENSG00000293080 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 = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000293080	ENST00000632456.2 link	n.769-13659A>G	intron_variant	Intron 6 of 6	6
ENSG00000293080	ENST00000756944.1 link	n.340-13659A>G	intron_variant	Intron 3 of 3
ENSG00000293080	ENST00000756945.1 link	n.519-13659A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21543

AN:

152030

Hom.:

2204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.0264

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.0675

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.0324

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.0793

Gnomad OTH

AF:

0.148

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

GnomAD4 genome

AF:

0.142

AC:

21574

AN:

152148

Hom.:

2208

Cov.:

AF XY:

0.141

AC XY:

10452

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.282

AC:

11719

AN:

41486

American (AMR)

AF:

0.148

AC:

2270

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

574

AN:

3470

East Asian (EAS)

AF:

0.0677

AC:

350

AN:

5172

South Asian (SAS)

AF:

0.115

AC:

554

AN:

4814

European-Finnish (FIN)

AF:

0.0324

AC:

343

AN:

10602

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0793

AC:

5391

AN:

68000

Other (OTH)

AF:

0.145

AC:

307

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

885

1770

2655

3540

4425

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.108

Hom.:

2804

Bravo

AF:

0.157

Asia WGS

AF:

0.106

AC:

372

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

5.2

(source)

DANN

Benign

0.54

PhyloP100

0.31

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