dbSNP rs12728740: 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:

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=-0.91).

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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