Genetic Variant ENST00000751816.1:n.108-29127G>A (chr1-159697400-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 ENST00000751816.1(ENSG00000297913):n.108-29127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,134 control chromosomes in the GnomAD database, including 1,667 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 0.13 ( 1667 hom., cov: 32)

Consequence

ENSG00000297913
ENST00000751816.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.06

Publications

6 publications found

Variant links:

Genes affected

ENSG00000297913 (HGNC:):

ENSG00000297913 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297913	ENST00000751816.1 link	n.108-29127G>A	intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1 link	n.110-29127G>A	intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1 link	n.63-29127G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19632

AN:

152016

Hom.:

1665

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0349

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.0345

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.133

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

GnomAD4 genome

AF:

0.129

AC:

19634

AN:

152134

Hom.:

1667

Cov.:

AF XY:

0.128

AC XY:

9497

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.0348

AC:

1446

AN:

41524

American (AMR)

AF:

0.128

AC:

1954

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

480

AN:

3472

East Asian (EAS)

AF:

0.0344

AC:

178

AN:

5176

South Asian (SAS)

AF:

0.129

AC:

620

AN:

4822

European-Finnish (FIN)

AF:

0.167

AC:

1767

AN:

10566

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.185

AC:

12563

AN:

67986

Other (OTH)

AF:

0.133

AC:

279

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

829

1658

2486

3315

4144

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<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:

0.164

Hom.:

2969

Bravo

AF:

0.121

Asia WGS

AF:

0.0660

AC:

231

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.4

(source)

DANN

Benign

0.66

PhyloP100

1.1

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