Genetic Variant ENST00000654191.1:n.517-1119C>T (chr10-64059007-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000654191.1(ENSG00000228566):n.517-1119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 152,208 control chromosomes in the GnomAD database, including 606 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 0.063 ( 606 hom., cov: 32)

Consequence

ENSG00000228566
ENST00000654191.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.269

Publications

1 publications found

Variant links:

Genes affected

ENSG00000228566 (HGNC:):

ENSG00000228566 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000654191.1, 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654191.1. 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
ENSG00000228566	ENST00000654191.1	n.517-1119C>T	intron	N/A
ENSG00000228566	ENST00000660795.1	n.266-1119C>T	intron	N/A
ENSG00000228566	ENST00000764129.1	n.211-1119C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0632

AC:

9607

AN:

152090

Hom.:

603

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.0588

Gnomad ASJ

AF:

0.0498

Gnomad EAS

AF:

0.0256

Gnomad SAS

AF:

0.0319

Gnomad FIN

AF:

0.00528

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0214

Gnomad OTH

AF:

0.0616

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

GnomAD4 genome

AF:

0.0633

AC:

9639

AN:

152208

Hom.:

606

Cov.:

AF XY:

0.0613

AC XY:

4560

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.159

AC:

6586

AN:

41512

American (AMR)

AF:

0.0591

AC:

903

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0498

AC:

173

AN:

3472

East Asian (EAS)

AF:

0.0259

AC:

134

AN:

5180

South Asian (SAS)

AF:

0.0311

AC:

150

AN:

4826

European-Finnish (FIN)

AF:

0.00528

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0214

AC:

1455

AN:

67992

Other (OTH)

AF:

0.0614

AC:

130

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

433

867

1300

1734

2167

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<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:

0.0334

Hom.:

119

Bravo

AF:

0.0733

Asia WGS

AF:

0.0420

AC:

145

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.8

(source)

DANN

Benign

0.59

PhyloP100

0.27

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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