Genetic Variant ENST00000846922.1:n.281-2295G>A (chr10-4014679-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 ENST00000846922.1(ENSG00000227101):n.281-2295G>A 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 152,178 control chromosomes in the GnomAD database, including 278 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 ( 278 hom., cov: 33)

Consequence

ENSG00000227101
ENST00000846922.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.242

Publications

4 publications found

Variant links:

Genes affected

ENSG00000227101 (HGNC:):

ENSG00000227101 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000227101	ENST00000846922.1 link	n.281-2295G>A	intron_variant	Intron 1 of 2
ENSG00000227101	ENST00000846923.1 link	n.249+9986G>A	intron_variant	Intron 1 of 1
ENSG00000227101	ENST00000846927.1 link	n.230-2295G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0540

AC:

8208

AN:

152060

Hom.:

279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0379

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.0477

Gnomad ASJ

AF:

0.0697

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.0671

Gnomad FIN

AF:

0.0227

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0603

Gnomad OTH

AF:

0.0598

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

GnomAD4 genome

AF:

0.0539

AC:

8210

AN:

152178

Hom.:

278

Cov.:

AF XY:

0.0531

AC XY:

3952

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0380

AC:

1576

AN:

41510

American (AMR)

AF:

0.0476

AC:

727

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0697

AC:

242

AN:

3472

East Asian (EAS)

AF:

0.157

AC:

813

AN:

5182

South Asian (SAS)

AF:

0.0678

AC:

327

AN:

4822

European-Finnish (FIN)

AF:

0.0227

AC:

240

AN:

10586

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0603

AC:

4101

AN:

67998

Other (OTH)

AF:

0.0587

AC:

124

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

411

822

1232

1643

2054

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<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:

0.0585

Hom.:

244

Bravo

AF:

0.0562

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.020

(source)

DANN

Benign

0.39

PhyloP100

-0.24

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