Genetic Variant SPRY4-AS1:n.138-29590A>G (chr5-142434380-A-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.138-29590A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,126 control chromosomes in the GnomAD database, including 6,225 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 ( 6225 hom., cov: 33)

Consequence

SPRY4-AS1
ENST00000414314.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.164

Publications

8 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 (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPRY4-AS1	NR_120664.1 link	n.507-29590A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SPRY4-AS1	ENST00000414314.2 link	n.138-29590A>G	intron_variant	Intron 1 of 3	3
SPRY4-AS1	ENST00000425963.1 link	n.137-29590A>G	intron_variant	Intron 1 of 2	3
SPRY4-AS1	ENST00000443800.5 link	n.154-29590A>G	intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39217

AN:

152006

Hom.:

6209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.377

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.680

Gnomad SAS

AF:

0.343

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.215

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

GnomAD4 genome

AF:

0.258

AC:

39280

AN:

152126

Hom.:

6225

Cov.:

AF XY:

0.263

AC XY:

19569

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.377

AC:

15630

AN:

41478

American (AMR)

AF:

0.213

AC:

3254

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

689

AN:

3470

East Asian (EAS)

AF:

0.680

AC:

3515

AN:

5166

South Asian (SAS)

AF:

0.342

AC:

1651

AN:

4822

European-Finnish (FIN)

AF:

0.202

AC:

2142

AN:

10600

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.172

AC:

11679

AN:

67986

Other (OTH)

AF:

0.222

AC:

468

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1400

2800

4199

5599

6999

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.204

Hom.:

10932

Bravo

AF:

0.264

Asia WGS

AF:

0.482

AC:

1673

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

6.7

(source)

DANN

Benign

0.72

PhyloP100

0.16

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