Genetic Variant STARD4-AS1:n.284-25958T>C (chr5-111643461-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 ENST00000500779.2(STARD4-AS1):n.284-25958T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,028 control chromosomes in the GnomAD database, including 5,912 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 0.27 ( 5912 hom., cov: 32)

Consequence

STARD4-AS1
ENST00000500779.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.372

Publications

6 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=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD4-AS1	NR_040093.1 link	n.284-25958T>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
STARD4-AS1	ENST00000500779.2 link	n.284-25958T>C	intron_variant	Intron 1 of 6	1
STARD4-AS1	ENST00000666013.1 link	n.2114-25958T>C	intron_variant	Intron 1 of 4
STARD4-AS1	ENST00000788272.1 link	n.294-25958T>C	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41410

AN:

151912

Hom.:

5886

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.357

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.266

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

GnomAD4 genome

AF:

0.273

AC:

41477

AN:

152028

Hom.:

5912

Cov.:

AF XY:

0.273

AC XY:

20288

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.316

AC:

13111

AN:

41466

American (AMR)

AF:

0.358

AC:

5473

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

679

AN:

3470

East Asian (EAS)

AF:

0.425

AC:

2192

AN:

5154

South Asian (SAS)

AF:

0.237

AC:

1143

AN:

4816

European-Finnish (FIN)

AF:

0.218

AC:

2306

AN:

10584

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.231

AC:

15701

AN:

67948

Other (OTH)

AF:

0.268

AC:

567

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1530

3060

4590

6120

7650

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.248

Hom.:

3947

Bravo

AF:

0.289

Asia WGS

AF:

0.312

AC:

1083

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.4

(source)

DANN

Benign

0.85

PhyloP100

-0.37

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