Genetic Variant SPRY4-AS1:n.227+19980T>G (chr5-142484039-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000414314.2(SPRY4-AS1):n.227+19980T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0617 in 152,330 control chromosomes in the GnomAD database, including 383 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 0.062 ( 383 hom., cov: 33)

Consequence

SPRY4-AS1
ENST00000414314.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.103

Publications

11 publications found

Variant links:

Genes affected

SPRY4-AS1 (HGNC:53465): (SPRY4 antisense RNA 1)

SPRY4-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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SPRY4-AS1	ENST00000414314.2 link	n.227+19980T>G	intron_variant	Intron 2 of 3	3
SPRY4-AS1	ENST00000425963.1 link	n.226+19980T>G	intron_variant	Intron 2 of 2	3
SPRY4-AS1	ENST00000443800.5 link	n.243+19980T>G	intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.0617

AC:

9396

AN:

152212

Hom.:

383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0151

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.0419

Gnomad ASJ

AF:

0.0510

Gnomad EAS

AF:

0.0542

Gnomad SAS

AF:

0.0852

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0863

Gnomad OTH

AF:

0.0630

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

GnomAD4 genome

AF:

0.0617

AC:

9399

AN:

152330

Hom.:

383

Cov.:

AF XY:

0.0633

AC XY:

4718

AN XY:

74492

show subpopulations

African (AFR)

AF:

0.0151

AC:

626

AN:

41576

American (AMR)

AF:

0.0419

AC:

642

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0510

AC:

177

AN:

3472

East Asian (EAS)

AF:

0.0545

AC:

283

AN:

5190

South Asian (SAS)

AF:

0.0853

AC:

412

AN:

4830

European-Finnish (FIN)

AF:

0.111

AC:

1181

AN:

10606

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0863

AC:

5873

AN:

68030

Other (OTH)

AF:

0.0624

AC:

132

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

459

918

1376

1835

2294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<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:

0.0733

Hom.:

993

Bravo

AF:

0.0523

Asia WGS

AF:

0.0710

AC:

245

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.2

(source)

DANN

Benign

0.58

PhyloP100

0.10

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