Genetic Variant ENSG00000257252:n.99-29221A>G (chr12-93033819-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 ENST00000549930.1(ENSG00000257252):n.99-29221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,134 control chromosomes in the GnomAD database, including 1,884 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 0.15 ( 1884 hom., cov: 32)

Consequence

ENSG00000257252
ENST00000549930.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.232

Publications

3 publications found

Variant links:

Genes affected

ENSG00000257252 (HGNC:):

ENSG00000257252 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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC643339	NR_040096.1 link	n.428-29221A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000257252	ENST00000549930.1 link	n.99-29221A>G	intron_variant	Intron 1 of 2	5
ENSG00000257252	ENST00000550324.7 link	n.169-29221A>G	intron_variant	Intron 1 of 2	3
ENSG00000257252	ENST00000754393.1 link	n.767-29221A>G	intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22875

AN:

152016

Hom.:

1879

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.0725

Gnomad AMR

AF:

0.0949

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.0979

Gnomad MID

AF:

0.201

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.150

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

GnomAD4 genome

AF:

0.151

AC:

22915

AN:

152134

Hom.:

1884

Cov.:

AF XY:

0.151

AC XY:

11240

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.213

AC:

8827

AN:

41476

American (AMR)

AF:

0.0948

AC:

1450

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

561

AN:

3472

East Asian (EAS)

AF:

0.155

AC:

801

AN:

5184

South Asian (SAS)

AF:

0.300

AC:

1442

AN:

4812

European-Finnish (FIN)

AF:

0.0979

AC:

1039

AN:

10610

Middle Eastern (MID)

AF:

0.199

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.123

AC:

8349

AN:

67972

Other (OTH)

AF:

0.152

AC:

322

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

959

1917

2876

3834

4793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.132

Hom.:

1767

Bravo

AF:

0.149

Asia WGS

AF:

0.222

AC:

771

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.9

(source)

DANN

Benign

0.45

PhyloP100

0.23

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