Genetic Variant ENST00000421825.2:n.188+5421C>T (chr7-120173815-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 ENST00000421825.2(ENSG00000233969):n.188+5421C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,012 control chromosomes in the GnomAD database, including 17,392 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 0.41 ( 17392 hom., cov: 32)

Consequence

ENSG00000233969
ENST00000421825.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.227

Publications

6 publications found

Variant links:

Genes affected

ENSG00000233969 (HGNC:):

ENSG00000233969 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000233969	ENST00000421825.2 link	n.188+5421C>T	intron_variant	Intron 2 of 3	3
ENSG00000233417	ENST00000456062.2 link	n.136-30719G>A	intron_variant	Intron 1 of 2	3
ENSG00000233417	ENST00000723829.1 link	n.259-32612G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

62392

AN:

151892

Hom.:

17348

Cov.:

show subpopulations

Gnomad AFR

AF:

0.785

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.328

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.373

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

GnomAD4 genome

AF:

0.411

AC:

62489

AN:

152012

Hom.:

17392

Cov.:

AF XY:

0.402

AC XY:

29897

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.786

AC:

32607

AN:

41490

American (AMR)

AF:

0.327

AC:

4988

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

913

AN:

3470

East Asian (EAS)

AF:

0.588

AC:

3034

AN:

5160

South Asian (SAS)

AF:

0.160

AC:

771

AN:

4818

European-Finnish (FIN)

AF:

0.213

AC:

2255

AN:

10564

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.248

AC:

16835

AN:

67934

Other (OTH)

AF:

0.376

AC:

795

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1448

2896

4343

5791

7239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

514

1028

1542

2056

2570

<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:

0.281

Hom.:

12228

Bravo

AF:

0.440

Asia WGS

AF:

0.454

AC:

1579

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.5

(source)

DANN

Benign

0.33

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