Genetic Variant ENST00000794751.1:n.393-30104C>T (chr1-60424002-G-A) – 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.393-30104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0685 in 151,966 control chromosomes in the GnomAD database, including 1,004 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 0.069 ( 1004 hom., cov: 32)

Consequence

ENSG00000303463
ENST00000794751.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.404

Publications

2 publications found

Variant links:

Genes affected

ENSG00000303463 (HGNC:):

ENSG00000303463 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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.393-30104C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0684

AC:

10390

AN:

151850

Hom.:

1002

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0391

Gnomad ASJ

AF:

0.00924

Gnomad EAS

AF:

0.0561

Gnomad SAS

AF:

0.0714

Gnomad FIN

AF:

0.00322

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00615

Gnomad OTH

AF:

0.0503

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

GnomAD4 genome

AF:

0.0685

AC:

10410

AN:

151966

Hom.:

1004

Cov.:

AF XY:

0.0681

AC XY:

5057

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.207

AC:

8554

AN:

41400

American (AMR)

AF:

0.0389

AC:

594

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.00924

AC:

AN:

3464

East Asian (EAS)

AF:

0.0562

AC:

291

AN:

5176

South Asian (SAS)

AF:

0.0719

AC:

345

AN:

4798

European-Finnish (FIN)

AF:

0.00322

AC:

AN:

10568

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00615

AC:

418

AN:

67988

Other (OTH)

AF:

0.0507

AC:

107

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

410

819

1229

1638

2048

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

106

212

318

424

530

<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:

0.0309

Hom.:

139

Bravo

AF:

0.0764

Asia WGS

AF:

0.0780

AC:

273

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

8.3

(source)

DANN

Benign

0.48

PhyloP100

0.40

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