Genetic Variant ENSG00000225718:n.360+3754C>T (chr7-69159355-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 ENST00000661243.1(ENSG00000225718):n.360+3754C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 152,272 control chromosomes in the GnomAD database, including 269 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 0.054 ( 269 hom., cov: 32)

Consequence

ENSG00000225718
ENST00000661243.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.495

Publications

4 publications found

Variant links:

Genes affected

ENSG00000225718 (HGNC:):

ENSG00000225718 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0786 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
ENSG00000225718	ENST00000661243.1 link	n.360+3754C>T		intron_variant	Intron 3 of 5
ENSG00000225718	ENST00000716162.1 link	n.1460-2229C>T		intron_variant	Intron 8 of 10

Frequencies

GnomAD3 genomes

AF:

0.0540

AC:

8217

AN:

152154

Hom.:

268

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0157

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0496

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0207

Gnomad FIN

AF:

0.0613

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0804

Gnomad OTH

AF:

0.0600

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

GnomAD4 genome

AF:

0.0539

AC:

8214

AN:

152272

Hom.:

269

Cov.:

AF XY:

0.0523

AC XY:

3892

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.0156

AC:

649

AN:

41576

American (AMR)

AF:

0.0495

AC:

757

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

424

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.0205

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.0613

AC:

650

AN:

10608

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0804

AC:

5466

AN:

68016

Other (OTH)

AF:

0.0589

AC:

124

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

407

814

1222

1629

2036

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0734

Hom.:

1241

Bravo

AF:

0.0517

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.58

(source)

DANN

Benign

0.79

PhyloP100

-0.49

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