Genetic Variant ENST00000473299.1:n.133-82818A>G (chr3-147239379-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000473299.1(ENSG00000243620):n.133-82818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,116 control chromosomes in the GnomAD database, including 227 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 0.044 ( 227 hom., cov: 32)

Consequence

ENSG00000243620
ENST00000473299.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.978

Publications

3 publications found

Variant links:

Genes affected

ENSG00000243620 (HGNC:):

ENSG00000243620 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0685 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
ENSG00000243620	ENST00000473299.1 link	n.133-82818A>G		intron_variant	Intron 2 of 5	4
ENSG00000243620	ENST00000670466.1 link	n.181-82818A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0443

AC:

6736

AN:

151998

Hom.:

227

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0109

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.0353

Gnomad ASJ

AF:

0.0488

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0132

Gnomad FIN

AF:

0.0457

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0702

Gnomad OTH

AF:

0.0518

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

GnomAD4 genome

AF:

0.0442

AC:

6731

AN:

152116

Hom.:

227

Cov.:

AF XY:

0.0419

AC XY:

3113

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.0109

AC:

453

AN:

41542

American (AMR)

AF:

0.0353

AC:

539

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0488

AC:

169

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5154

South Asian (SAS)

AF:

0.0126

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0457

AC:

484

AN:

10600

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0702

AC:

4768

AN:

67924

Other (OTH)

AF:

0.0512

AC:

108

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

334

668

1001

1335

1669

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<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:

0.0633

Hom.:

569

Bravo

AF:

0.0426

Asia WGS

AF:

0.00609

AC:

AN:

3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

0.98

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