Genetic Variant ENST00000425900.1:n.81+13408C>T (chr20-7083102-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000425900.1(ENSG00000232271):n.81+13408C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 151,860 control chromosomes in the GnomAD database, including 1,054 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 0.072 ( 1054 hom., cov: 32)

Consequence

ENSG00000232271
ENST00000425900.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.406

Publications

1 publications found

Variant links:

Genes affected

ENSG00000232271 (HGNC:):

ENSG00000232271 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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
ENSG00000232271	ENST00000425900.1 link	n.81+13408C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.0718

AC:

10889

AN:

151742

Hom.:

1049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0363

Gnomad ASJ

AF:

0.0257

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.00788

Gnomad FIN

AF:

0.00274

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0122

Gnomad OTH

AF:

0.0644

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

GnomAD4 genome

AF:

0.0719

AC:

10914

AN:

151860

Hom.:

1054

Cov.:

AF XY:

0.0699

AC XY:

5186

AN XY:

74228

show subpopulations

African (AFR)

AF:

0.223

AC:

9224

AN:

41398

American (AMR)

AF:

0.0360

AC:

548

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.0257

AC:

AN:

3468

East Asian (EAS)

AF:

0.00194

AC:

AN:

5166

South Asian (SAS)

AF:

0.00789

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.00274

AC:

AN:

10596

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0122

AC:

830

AN:

67894

Other (OTH)

AF:

0.0637

AC:

134

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

449

897

1346

1794

2243

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0901

Hom.:

552

Bravo

AF:

0.0833

Asia WGS

AF:

0.0250

AC:

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

1.7

(source)

DANN

Benign

0.74

PhyloP100

-0.41

Mutation Taster

=100/0

polymorphism

(source)

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