Genetic Variant ENST00000724731.1:n.109+258T>C (chr17-30237328-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000724731.1(ENSG00000266120):n.109+258T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.19 ( 468 hom., cov: 4)

Consequence

ENSG00000266120
ENST00000724731.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.732

Publications

749 publications found

Variant links:

Genes affected

ENSG00000266120 (HGNC:):

ENSG00000266120 links:

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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=-0.67).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724731.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266120	ENST00000724731.1		n.109+258T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

5881

AN:

31434

Hom.:

464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.292

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.0853

Gnomad EAS

AF:

0.318

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.0938

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.187

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

GnomAD4 genome

AF:

0.187

AC:

5896

AN:

31456

Hom.:

468

Cov.:

AF XY:

0.196

AC XY:

2750

AN XY:

13996

show subpopulations

African (AFR)

AF:

0.293

AC:

2651

AN:

9038

American (AMR)

AF:

0.179

AC:

344

AN:

1918

Ashkenazi Jewish (ASJ)

AF:

0.0853

AC:

AN:

844

East Asian (EAS)

AF:

0.321

AC:

193

AN:

602

South Asian (SAS)

AF:

0.292

AC:

158

AN:

542

European-Finnish (FIN)

AF:

0.192

AC:

215

AN:

1120

Middle Eastern (MID)

AF:

0.100

AC:

AN:

European-Non Finnish (NFE)

AF:

0.129

AC:

2161

AN:

16750

Other (OTH)

AF:

0.186

AC:

AN:

404

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

246

493

739

986

1232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<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:

0.0264

Hom.:

Bravo

AF:

0.119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

5.5

(source)

DANN

Benign

0.41

PhyloP100

-0.73

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over