Genetic Variant ENSG00000286340:n.317-58821T>C (chr6-79143023-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 ENST00000759658.1(ENSG00000286340):n.317-58821T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,934 control chromosomes in the GnomAD database, including 5,331 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 0.26 ( 5331 hom., cov: 32)

Consequence

ENSG00000286340
ENST00000759658.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286340 (HGNC:):

ENSG00000286340 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 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
ENSG00000286340	ENST00000759658.1 link	n.317-58821T>C		intron_variant	Intron 2 of 2
ENSG00000286340	ENST00000759659.1 link	n.179-37464T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.256

AC:

38854

AN:

151816

Hom.:

5332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.223

Gnomad EAS

AF:

0.190

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.330

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.269

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

GnomAD4 genome

AF:

0.256

AC:

38865

AN:

151934

Hom.:

5331

Cov.:

AF XY:

0.255

AC XY:

18942

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.166

AC:

6871

AN:

41484

American (AMR)

AF:

0.286

AC:

4366

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.223

AC:

772

AN:

3468

East Asian (EAS)

AF:

0.190

AC:

977

AN:

5144

South Asian (SAS)

AF:

0.163

AC:

787

AN:

4820

European-Finnish (FIN)

AF:

0.330

AC:

3488

AN:

10564

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.304

AC:

20654

AN:

67902

Other (OTH)

AF:

0.266

AC:

560

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1493

2985

4478

5970

7463

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.282

Hom.:

1078

Bravo

AF:

0.251

Asia WGS

AF:

0.162

AC:

563

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.27

(source)

DANN

Benign

0.41

PhyloP100

-1.2

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