Genetic Variant ENSG00000243276:n.232+23167A>T (chr3-118473456-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000482142.5(ENSG00000243276):n.232+23167A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 151,914 control chromosomes in the GnomAD database, including 39,480 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 0.71 ( 39480 hom., cov: 31)

Consequence

ENSG00000243276
ENST00000482142.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.430

Publications

3 publications found

Variant links:

Genes affected

ENSG00000243276 (HGNC:):

ENSG00000243276 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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
ENSG00000243276	ENST00000482142.5 link	n.232+23167A>T	intron_variant	Intron 3 of 6	5
ENSG00000243276	ENST00000833975.1 link	n.448+23167A>T	intron_variant	Intron 5 of 5
ENSG00000243276	ENST00000833976.1 link	n.349+23167A>T	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.711

AC:

107932

AN:

151796

Hom.:

39466

Cov.:

show subpopulations

Gnomad AFR

AF:

0.512

Gnomad AMI

AF:

0.880

Gnomad AMR

AF:

0.741

Gnomad ASJ

AF:

0.761

Gnomad EAS

AF:

0.922

Gnomad SAS

AF:

0.819

Gnomad FIN

AF:

0.760

Gnomad MID

AF:

0.813

Gnomad NFE

AF:

0.788

Gnomad OTH

AF:

0.753

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

GnomAD4 genome

AF:

0.711

AC:

107994

AN:

151914

Hom.:

39480

Cov.:

AF XY:

0.716

AC XY:

53168

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.511

AC:

21163

AN:

41378

American (AMR)

AF:

0.741

AC:

11312

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.761

AC:

2637

AN:

3466

East Asian (EAS)

AF:

0.922

AC:

4761

AN:

5164

South Asian (SAS)

AF:

0.820

AC:

3942

AN:

4808

European-Finnish (FIN)

AF:

0.760

AC:

8019

AN:

10554

Middle Eastern (MID)

AF:

0.810

AC:

238

AN:

294

European-Non Finnish (NFE)

AF:

0.788

AC:

53529

AN:

67964

Other (OTH)

AF:

0.755

AC:

1590

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1472

2943

4415

5886

7358

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

836

1672

2508

3344

4180

<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:

0.743

Hom.:

5299

Bravo

AF:

0.701

Asia WGS

AF:

0.828

AC:

2880

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.34

(source)

DANN

Benign

0.76

PhyloP100

-0.43

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