Genetic Variant ENSG00000302692:n.483-7715T>C (chr4-68776903-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 ENST00000788926.1(ENSG00000302692):n.483-7715T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 149,790 control chromosomes in the GnomAD database, including 8,285 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 0.25 ( 8285 hom., cov: 31)

Consequence

ENSG00000302692
ENST00000788926.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.837

Publications

3 publications found

Variant links:

Genes affected

ENSG00000302692 (HGNC:):

ENSG00000302692 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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
ENSG00000302692	ENST00000788926.1 link	n.483-7715T>C		intron_variant	Intron 4 of 6
ENSG00000302692	ENST00000788927.1 link	n.61-7715T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

37556

AN:

149674

Hom.:

8256

Cov.:

show subpopulations

Gnomad AFR

AF:

0.591

Gnomad AMI

AF:

0.0736

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.321

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.0716

Gnomad MID

AF:

0.128

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.220

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

GnomAD4 genome

AF:

0.251

AC:

37637

AN:

149790

Hom.:

8285

Cov.:

AF XY:

0.245

AC XY:

18134

AN XY:

74038

show subpopulations

African (AFR)

AF:

0.591

AC:

24410

AN:

41298

American (AMR)

AF:

0.179

AC:

2709

AN:

15168

Ashkenazi Jewish (ASJ)

AF:

0.100

AC:

336

AN:

3346

East Asian (EAS)

AF:

0.320

AC:

1628

AN:

5082

South Asian (SAS)

AF:

0.108

AC:

518

AN:

4808

European-Finnish (FIN)

AF:

0.0716

AC:

755

AN:

10552

Middle Eastern (MID)

AF:

0.134

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.101

AC:

6712

AN:

66246

Other (OTH)

AF:

0.222

AC:

463

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1054

2109

3163

4218

5272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

330

660

990

1320

1650

<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:

0.197

Hom.:

745

Bravo

AF:

0.275

Asia WGS

AF:

0.235

AC:

818

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

1.6

(source)

DANN

Benign

0.63

PhyloP100

-0.84

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