Genetic Variant ENSG00000257239:n.472-30487T>C (chr12-41860412-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000550874.1(ENSG00000257239):n.472-30487T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,206 control chromosomes in the GnomAD database, including 1,520 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 0.14 ( 1520 hom., cov: 32)

Consequence

ENSG00000257239
ENST00000550874.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.151

Publications

1 publications found

Variant links:

Genes affected

ENSG00000257239 (HGNC:):

ENSG00000257239 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=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.164 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
ENSG00000257239	ENST00000550874.1 link	n.472-30487T>C		intron_variant	Intron 1 of 1	3
ENSG00000257239	ENST00000824751.1 link	n.123-30487T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21520

AN:

152088

Hom.:

1518

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.140

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.136

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

GnomAD4 genome

AF:

0.141

AC:

21523

AN:

152206

Hom.:

1520

Cov.:

AF XY:

0.142

AC XY:

10598

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.140

AC:

5809

AN:

41544

American (AMR)

AF:

0.140

AC:

2135

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

449

AN:

3472

East Asian (EAS)

AF:

0.172

AC:

887

AN:

5166

South Asian (SAS)

AF:

0.173

AC:

836

AN:

4822

European-Finnish (FIN)

AF:

0.127

AC:

1350

AN:

10594

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9606

AN:

68012

Other (OTH)

AF:

0.134

AC:

283

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

953

1906

2859

3812

4765

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.141

Hom.:

1018

Bravo

AF:

0.141

Asia WGS

AF:

0.148

AC:

514

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.7

(source)

DANN

Benign

0.73

PhyloP100

-0.15

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