Genetic Variant ENSG00000297913:n.*39C>A (chr1-159740303-C-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.*39C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,118 control chromosomes in the GnomAD database, including 6,531 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 0.26 ( 6531 hom., cov: 32)

Consequence

ENSG00000297913
ENST00000751816.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.134

Publications

4 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000297913	ENST00000751816.1 link	n.*39C>A	downstream_gene_variant
ENSG00000297913	ENST00000751817.1 link	n.*216C>A	downstream_gene_variant
ENSG00000297913	ENST00000751818.1 link	n.*214C>A	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39634

AN:

152000

Hom.:

6530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0687

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.304

Gnomad EAS

AF:

0.0582

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.459

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.342

Gnomad OTH

AF:

0.265

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

GnomAD4 genome

AF:

0.261

AC:

39648

AN:

152118

Hom.:

6531

Cov.:

AF XY:

0.267

AC XY:

19867

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.0686

AC:

2848

AN:

41538

American (AMR)

AF:

0.332

AC:

5076

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.304

AC:

1056

AN:

3468

East Asian (EAS)

AF:

0.0582

AC:

301

AN:

5176

South Asian (SAS)

AF:

0.282

AC:

1363

AN:

4828

European-Finnish (FIN)

AF:

0.459

AC:

4835

AN:

10544

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.342

AC:

23219

AN:

67972

Other (OTH)

AF:

0.265

AC:

560

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1374

2749

4123

5498

6872

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

408

816

1224

1632

2040

<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:

0.309

Hom.:

9485

Bravo

AF:

0.244

Asia WGS

AF:

0.176

AC:

612

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

4.0

(source)

DANN

Benign

0.77

PhyloP100

-0.13

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