Genetic Variant ENST00000773840.1:n.232-1100G>A (chr22-49287979-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000773840.1(ENSG00000300754):n.232-1100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,152 control chromosomes in the GnomAD database, including 4,810 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 0.23 ( 4810 hom., cov: 33)

Consequence

ENSG00000300754
ENST00000773840.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.469

Publications

2 publications found

Variant links:

Genes affected

ENSG00000300754 (HGNC:):

ENSG00000300754 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000300754	ENST00000773840.1 link	n.232-1100G>A	intron_variant	Intron 2 of 4
ENSG00000300754	ENST00000773841.1 link	n.102-1100G>A	intron_variant	Intron 1 of 3
ENSG00000300754	ENST00000773842.1 link	n.184-1100G>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34366

AN:

152034

Hom.:

4803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0624

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.379

Gnomad EAS

AF:

0.162

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.237

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.312

Gnomad OTH

AF:

0.242

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

GnomAD4 genome

AF:

0.226

AC:

34366

AN:

152152

Hom.:

4810

Cov.:

AF XY:

0.222

AC XY:

16545

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0622

AC:

2582

AN:

41514

American (AMR)

AF:

0.256

AC:

3906

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

1313

AN:

3468

East Asian (EAS)

AF:

0.162

AC:

837

AN:

5178

South Asian (SAS)

AF:

0.261

AC:

1260

AN:

4824

European-Finnish (FIN)

AF:

0.237

AC:

2503

AN:

10582

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.312

AC:

21184

AN:

67988

Other (OTH)

AF:

0.240

AC:

506

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1296

2593

3889

5186

6482

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.287

Hom.:

11120

Bravo

AF:

0.218

Asia WGS

AF:

0.192

AC:

669

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.0

(source)

DANN

Benign

0.77

PhyloP100

-0.47

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