Genetic Variant ENST00000592441.1:n.172+28109C>T (chr7-106732457-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000592441.1(ENSG00000243797):n.172+28109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,996 control chromosomes in the GnomAD database, including 13,244 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 ( 13239 hom., cov: 31)

Exomes 𝑓: 0.50 ( 5 hom. )

Consequence

ENSG00000243797
ENST00000592441.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.103

Publications

17 publications found

Variant links:

Genes affected

ENSG00000243797 (HGNC:):

ENSG00000243797 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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
ENSG00000243797	ENST00000592441.1 link	n.172+28109C>T		intron_variant	Intron 2 of 4	2
ENSG00000243797	ENST00000490856.5 link	n.-8C>T		upstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.412

AC:

62533

AN:

151852

Hom.:

13221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.497

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.362

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.405

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.412

AC:

62588

AN:

151970

Hom.:

13239

Cov.:

AF XY:

0.410

AC XY:

30434

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.371

AC:

15360

AN:

41416

American (AMR)

AF:

0.365

AC:

5578

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.497

AC:

1722

AN:

3468

East Asian (EAS)

AF:

0.231

AC:

1193

AN:

5164

South Asian (SAS)

AF:

0.361

AC:

1737

AN:

4816

European-Finnish (FIN)

AF:

0.473

AC:

5001

AN:

10570

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.453

AC:

30778

AN:

67962

Other (OTH)

AF:

0.401

AC:

846

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1859

3719

5578

7438

9297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

594

1188

1782

2376

2970

<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:

0.434

Hom.:

35344

Bravo

AF:

0.401

Asia WGS

AF:

0.324

AC:

1129

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.3

(source)

DANN

Benign

0.50

PhyloP100

0.10

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