Genetic Variant SPRY4-AS1:n.228-41272C>T (chr5-142540530-C-T) – 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.228-41272C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,850 control chromosomes in the GnomAD database, including 5,571 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 0.21 ( 5571 hom., cov: 31)

Consequence

SPRY4-AS1
ENST00000414314.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106

Publications

2 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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.228-41272C>T	intron_variant	Intron 2 of 3	3
SPRY4-AS1	ENST00000443800.5 link	n.244-41272C>T	intron_variant	Intron 2 of 3	3
SPRY4-AS1	ENST00000510311.6 link	n.597-41272C>T	intron_variant	Intron 4 of 7	4

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31714

AN:

151728

Hom.:

5559

Cov.:

show subpopulations

Gnomad AFR

AF:

0.455

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.252

Gnomad FIN

AF:

0.0875

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.0800

Gnomad OTH

AF:

0.176

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

GnomAD4 genome

AF:

0.209

AC:

31763

AN:

151850

Hom.:

5571

Cov.:

AF XY:

0.210

AC XY:

15612

AN XY:

74220

show subpopulations

African (AFR)

AF:

0.455

AC:

18795

AN:

41336

American (AMR)

AF:

0.128

AC:

1951

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.105

AC:

365

AN:

3470

East Asian (EAS)

AF:

0.510

AC:

2625

AN:

5148

South Asian (SAS)

AF:

0.252

AC:

1209

AN:

4792

European-Finnish (FIN)

AF:

0.0875

AC:

924

AN:

10558

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0799

AC:

5434

AN:

67970

Other (OTH)

AF:

0.179

AC:

376

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1015

2031

3046

4062

5077

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

314

628

942

1256

1570

<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:

0.112

Hom.:

2795

Bravo

AF:

0.222

Asia WGS

AF:

0.379

AC:

1318

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

-0.11

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