Genetic Variant ENSG00000234426:n.90+17846G>A (chr6-88403098-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000429137.1(ENSG00000234426):n.90+17846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,054 control chromosomes in the GnomAD database, including 1,722 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 0.13 ( 1722 hom., cov: 31)

Consequence

ENSG00000234426
ENST00000429137.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.684

Publications

18 publications found

Variant links:

Genes affected

ENSG00000234426 (HGNC:):

ENSG00000234426 links:

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new If you want to explore the variant's impact on the transcript ENST00000429137.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429137.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000234426	ENST00000429137.1	TSL:3	n.90+17846G>A	intron	N/A
ENSG00000234426	ENST00000648572.1		n.27+17846G>A	intron	N/A
ENSG00000234426	ENST00000655924.1		n.330+38986G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.132

AC:

20041

AN:

151936

Hom.:

1717

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0317

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.0815

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.174

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

GnomAD4 genome

AF:

0.132

AC:

20056

AN:

152054

Hom.:

1722

Cov.:

AF XY:

0.133

AC XY:

9862

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.0317

AC:

1315

AN:

41490

American (AMR)

AF:

0.222

AC:

3390

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

561

AN:

3468

East Asian (EAS)

AF:

0.290

AC:

1495

AN:

5152

South Asian (SAS)

AF:

0.229

AC:

1102

AN:

4806

European-Finnish (FIN)

AF:

0.0815

AC:

863

AN:

10584

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10705

AN:

67974

Other (OTH)

AF:

0.173

AC:

364

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

850

1700

2549

3399

4249

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.152

Hom.:

6626

Bravo

AF:

0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

9.3

(source)

DANN

Benign

0.63

PhyloP100

0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over