Genetic Variant ENSG00000231902:n.477+8534T>G (chr9-7952034-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000656028.1(ENSG00000231902):n.477+8534T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,706 control chromosomes in the GnomAD database, including 3,918 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 0.20 ( 3918 hom., cov: 31)

Consequence

ENSG00000231902
ENST00000656028.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.430

Publications

0 publications found

Variant links:

Genes affected

ENSG00000231902 (HGNC:):

ENSG00000231902 links:

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new If you want to explore the variant's impact on the transcript ENST00000656028.1, 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656028.1. 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	HGVSc	Effect	Exon Rank
ENSG00000231902	ENST00000656028.1	n.477+8534T>G	intron	N/A
ENSG00000231902	ENST00000668681.2	n.400+8796T>G	intron	N/A
ENSG00000231902	ENST00000813700.1	n.400+8796T>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

30374

AN:

151588

Hom.:

3923

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0457

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.305

Gnomad EAS

AF:

0.459

Gnomad SAS

AF:

0.346

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.222

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

GnomAD4 genome

AF:

0.200

AC:

30368

AN:

151706

Hom.:

3918

Cov.:

AF XY:

0.204

AC XY:

15150

AN XY:

74114

show subpopulations

African (AFR)

AF:

0.0455

AC:

1887

AN:

41444

American (AMR)

AF:

0.306

AC:

4647

AN:

15190

Ashkenazi Jewish (ASJ)

AF:

0.305

AC:

1057

AN:

3466

East Asian (EAS)

AF:

0.459

AC:

2336

AN:

5092

South Asian (SAS)

AF:

0.346

AC:

1661

AN:

4802

European-Finnish (FIN)

AF:

0.172

AC:

1812

AN:

10536

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.239

AC:

16202

AN:

67864

Other (OTH)

AF:

0.221

AC:

465

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1128

2257

3385

4514

5642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

328

656

984

1312

1640

<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:

0.206

Hom.:

472

Bravo

AF:

0.203

Asia WGS

AF:

0.342

AC:

1186

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.4

(source)

DANN

Benign

0.53

PhyloP100

0.43

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