Genetic Variant STARD4-AS1:n.284-65799C>A (chr5-111603620-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000500779.2(STARD4-AS1):n.284-65799C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0285 in 152,320 control chromosomes in the GnomAD database, including 124 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 0.029 ( 124 hom., cov: 33)

Consequence

STARD4-AS1
ENST00000500779.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.287

Publications

1 publications found

Variant links:

Genes affected

STARD4-AS1 (HGNC:44117): (STARD4 antisense RNA 1)

STARD4-AS1 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=-0.8).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD4-AS1	NR_040093.1 link	n.284-65799C>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
STARD4-AS1	ENST00000500779.2 link	n.284-65799C>A	intron_variant	Intron 1 of 6	1
STARD4-AS1	ENST00000666013.1 link	n.2114-65799C>A	intron_variant	Intron 1 of 4
STARD4-AS1	ENST00000788272.1 link	n.294-65799C>A	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.0286

AC:

4347

AN:

152202

Hom.:

123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0369

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0964

Gnomad ASJ

AF:

0.0113

Gnomad EAS

AF:

0.0745

Gnomad SAS

AF:

0.0325

Gnomad FIN

AF:

0.00424

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.00930

Gnomad OTH

AF:

0.0315

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

GnomAD4 genome

AF:

0.0285

AC:

4348

AN:

152320

Hom.:

124

Cov.:

AF XY:

0.0301

AC XY:

2245

AN XY:

74482

show subpopulations

African (AFR)

AF:

0.0368

AC:

1530

AN:

41564

American (AMR)

AF:

0.0962

AC:

1471

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0113

AC:

AN:

3466

East Asian (EAS)

AF:

0.0745

AC:

387

AN:

5194

South Asian (SAS)

AF:

0.0325

AC:

157

AN:

4826

European-Finnish (FIN)

AF:

0.00424

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00930

AC:

633

AN:

68036

Other (OTH)

AF:

0.0331

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

219

439

658

878

1097

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<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:

0.0318

Hom.:

Bravo

AF:

0.0351

Asia WGS

AF:

0.0640

AC:

221

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.7

(source)

DANN

Benign

0.62

PhyloP100

-0.29

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