Genetic Variant ENSG00000243276:n.232+52847A>G (chr3-118443776-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 ENST00000482142.5(ENSG00000243276):n.232+52847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,218 control chromosomes in the GnomAD database, including 2,062 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 0.16 ( 2062 hom., cov: 33)

Consequence

ENSG00000243276
ENST00000482142.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0660

Publications

7 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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+52847A>G	intron_variant	Intron 3 of 6	5
ENSG00000243276	ENST00000833975.1 link	n.448+52847A>G	intron_variant	Intron 5 of 5
ENSG00000243276	ENST00000833976.1 link	n.349+52847A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

24015

AN:

152100

Hom.:

2059

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.0217

Gnomad SAS

AF:

0.0935

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.158

AC:

24035

AN:

152218

Hom.:

2062

Cov.:

AF XY:

0.154

AC XY:

11475

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.206

AC:

8561

AN:

41514

American (AMR)

AF:

0.111

AC:

1702

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.226

AC:

785

AN:

3472

East Asian (EAS)

AF:

0.0216

AC:

112

AN:

5184

South Asian (SAS)

AF:

0.0938

AC:

452

AN:

4818

European-Finnish (FIN)

AF:

0.136

AC:

1444

AN:

10620

Middle Eastern (MID)

AF:

0.250

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.153

AC:

10391

AN:

68000

Other (OTH)

AF:

0.155

AC:

327

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1040

2080

3120

4160

5200

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.154

Hom.:

6377

Bravo

AF:

0.159

Asia WGS

AF:

0.0900

AC:

315

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.8

(source)

DANN

Benign

0.73

PhyloP100

-0.066

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