Genetic Variant ENSG00000266120:n.109+82G>A (chr17-30237152-G-A) – 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+82G>A 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 0.063 ( 318 hom., cov: 9)

Consequence

ENSG00000266120
ENST00000724731.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.85

Publications

57 publications found

Variant links:

Genes affected

ENSG00000266120 (HGNC:):

ENSG00000266120 links:

Genome browser will be placed here

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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371720	XR_001752824.2 link	n.280+82G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266120	ENST00000724731.1 link	n.109+82G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.0630

AC:

4113

AN:

65304

Hom.:

318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0136

Gnomad AMI

AF:

0.0930

Gnomad AMR

AF:

0.0327

Gnomad ASJ

AF:

0.0815

Gnomad EAS

AF:

0.000842

Gnomad SAS

AF:

0.0411

Gnomad FIN

AF:

0.0672

Gnomad MID

AF:

0.0215

Gnomad NFE

AF:

0.100

Gnomad OTH

AF:

0.0420

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

GnomAD4 genome

AF:

0.0629

AC:

4111

AN:

65326

Hom.:

318

Cov.:

AF XY:

0.0588

AC XY:

1824

AN XY:

31030

show subpopulations

African (AFR)

AF:

0.0135

AC:

208

AN:

15356

American (AMR)

AF:

0.0326

AC:

256

AN:

7844

Ashkenazi Jewish (ASJ)

AF:

0.0815

AC:

148

AN:

1816

East Asian (EAS)

AF:

0.000845

AC:

AN:

2368

South Asian (SAS)

AF:

0.0412

AC:

AN:

1530

European-Finnish (FIN)

AF:

0.0672

AC:

289

AN:

4302

Middle Eastern (MID)

AF:

0.0230

AC:

AN:

174

European-Non Finnish (NFE)

AF:

0.100

AC:

3067

AN:

30652

Other (OTH)

AF:

0.0418

AC:

AN:

886

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.536

Heterozygous variant carriers

168

337

505

674

842

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<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:

0.116

Hom.:

1720

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.9

(source)

DANN

Benign

0.55

PhyloP100

-1.8

Splicing

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over