Genetic Variant ENSG00000285471:c.-524+10226C>T (chr17-5783253-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000573619.1(ENSG00000285471):c.-524+10226C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,056 control chromosomes in the GnomAD database, including 47,993 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 0.78 ( 47993 hom., cov: 30)

Consequence

ENSG00000285471
ENST00000573619.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69

Publications

3 publications found

Variant links:

Genes affected

ENSG00000285471 (HGNC:):

ENSG00000285471 links:

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new If you want to explore the variant's impact on the transcript ENST00000573619.1, 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 (NFE) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000573619.1. 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
	LOC339166	NR_040000.1		n.794+10226C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285471	ENST00000573619.1	TSL:2	c.-524+10226C>T		intron	N/A	ENSP00000461865.1	I3NI40
	ENSG00000284837	ENST00000563763.5	TSL:1	n.794+10226C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.783

AC:

118977

AN:

151938

Hom.:

47960

Cov.:

show subpopulations

Gnomad AFR

AF:

0.666

Gnomad AMI

AF:

0.942

Gnomad AMR

AF:

0.833

Gnomad ASJ

AF:

0.775

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.522

Gnomad FIN

AF:

0.883

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.879

Gnomad OTH

AF:

0.791

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

GnomAD4 genome

AF:

0.783

AC:

119058

AN:

152056

Hom.:

47993

Cov.:

AF XY:

0.774

AC XY:

57547

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.665

AC:

27575

AN:

41442

American (AMR)

AF:

0.833

AC:

12735

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.775

AC:

2686

AN:

3468

East Asian (EAS)

AF:

0.329

AC:

1705

AN:

5180

South Asian (SAS)

AF:

0.524

AC:

2504

AN:

4780

European-Finnish (FIN)

AF:

0.883

AC:

9344

AN:

10584

Middle Eastern (MID)

AF:

0.779

AC:

229

AN:

294

European-Non Finnish (NFE)

AF:

0.879

AC:

59750

AN:

67998

Other (OTH)

AF:

0.791

AC:

1673

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1173

2347

3520

4694

5867

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

840

1680

2520

3360

4200

<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:

0.834

Hom.:

143099

Bravo

AF:

0.774

Asia WGS

AF:

0.488

AC:

1699

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

0.35

(source)

DANN

Benign

0.60

PhyloP100

-1.7

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