Genetic Variant ENST00000654217.1:n.153+7081G>A (chr1-58553401-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 ENST00000654217.1(ENSG00000286918):n.153+7081G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,058 control chromosomes in the GnomAD database, including 3,677 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 0.17 ( 3676 hom., cov: 32)

Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

ENSG00000286918
ENST00000654217.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.65

Publications

4 publications found

Variant links:

Genes affected

ENSG00000286918 (HGNC:):

ENSG00000286918 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286918	ENST00000654217.1 link	n.153+7081G>A		intron_variant	Intron 1 of 1
ENSG00000270209	ENST00000604022.1 link	n.-68C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26509

AN:

151934

Hom.:

3656

Cov.:

show subpopulations

Gnomad AFR

AF:

0.385

Gnomad AMI

AF:

0.142

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.00269

Gnomad SAS

AF:

0.0547

Gnomad FIN

AF:

0.0791

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.164

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.175

AC:

26566

AN:

152052

Hom.:

3676

Cov.:

AF XY:

0.169

AC XY:

12548

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.386

AC:

15964

AN:

41398

American (AMR)

AF:

0.113

AC:

1727

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

371

AN:

3466

East Asian (EAS)

AF:

0.00270

AC:

AN:

5186

South Asian (SAS)

AF:

0.0560

AC:

270

AN:

4818

European-Finnish (FIN)

AF:

0.0791

AC:

837

AN:

10582

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6858

AN:

67990

Other (OTH)

AF:

0.162

AC:

343

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

985

1970

2955

3940

4925

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.153

Hom.:

352

Bravo

AF:

0.187

Asia WGS

AF:

0.0640

AC:

222

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.025

(source)

DANN

Benign

0.51

PhyloP100

-4.6

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