Genetic Variant ENSG00000306126:n.220-23754A>T (chr17-41036545-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000815517.1(ENSG00000306126):n.220-23754A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0708 in 152,182 control chromosomes in the GnomAD database, including 754 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 0.071 ( 754 hom., cov: 32)

Consequence

ENSG00000306126
ENST00000815517.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

1 publications found

Variant links:

Genes affected

ENSG00000306126 (HGNC:):

ENSG00000306126 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000306126	ENST00000815517.1 link	n.220-23754A>T	intron_variant	Intron 2 of 2
ENSG00000306126	ENST00000815518.1 link	n.160-23754A>T	intron_variant	Intron 1 of 1
ENSG00000306126	ENST00000815519.1 link	n.332+2473A>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0707

AC:

10754

AN:

152064

Hom.:

753

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.0242

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.0242

Gnomad FIN

AF:

0.0309

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0133

Gnomad OTH

AF:

0.0684

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

GnomAD4 genome

AF:

0.0708

AC:

10774

AN:

152182

Hom.:

754

Cov.:

AF XY:

0.0718

AC XY:

5343

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.161

AC:

6682

AN:

41476

American (AMR)

AF:

0.107

AC:

1629

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0242

AC:

AN:

3470

East Asian (EAS)

AF:

0.163

AC:

846

AN:

5184

South Asian (SAS)

AF:

0.0228

AC:

110

AN:

4822

European-Finnish (FIN)

AF:

0.0309

AC:

328

AN:

10612

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0133

AC:

904

AN:

68008

Other (OTH)

AF:

0.0691

AC:

146

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

474

948

1423

1897

2371

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0116

Hom.:

Bravo

AF:

0.0833

Asia WGS

AF:

0.117

AC:

405

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.15

(source)

DANN

Benign

0.36

PhyloP100

-1.0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over