dbSNP rs152439: SPRY4-AS1:n.228-36972T>C (chr5-142544830-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 ENST00000414314.2(SPRY4-AS1):n.228-36972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,798 control chromosomes in the GnomAD database, including 8,729 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 0.23 ( 8729 hom., cov: 32)

Consequence

SPRY4-AS1
ENST00000414314.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.59

Publications

7 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 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.228-36972T>C	intron_variant	Intron 2 of 3	3
SPRY4-AS1	ENST00000443800.5 link	n.244-36972T>C	intron_variant	Intron 2 of 3	3
SPRY4-AS1	ENST00000510311.6 link	n.597-36972T>C	intron_variant	Intron 4 of 7	4

Frequencies

GnomAD3 genomes

AF:

0.231

AC:

35063

AN:

151682

Hom.:

8704

Cov.:

show subpopulations

Gnomad AFR

AF:

0.627

Gnomad AMI

AF:

0.0418

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.0467

Gnomad EAS

AF:

0.0701

Gnomad SAS

AF:

0.0964

Gnomad FIN

AF:

0.0838

Gnomad MID

AF:

0.143

Gnomad NFE

AF:

0.0739

Gnomad OTH

AF:

0.181

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

GnomAD4 genome

AF:

0.231

AC:

35133

AN:

151798

Hom.:

8729

Cov.:

AF XY:

0.225

AC XY:

16710

AN XY:

74204

show subpopulations

African (AFR)

AF:

0.627

AC:

25932

AN:

41378

American (AMR)

AF:

0.122

AC:

1856

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0467

AC:

162

AN:

3466

East Asian (EAS)

AF:

0.0703

AC:

360

AN:

5122

South Asian (SAS)

AF:

0.0957

AC:

459

AN:

4798

European-Finnish (FIN)

AF:

0.0838

AC:

884

AN:

10544

Middle Eastern (MID)

AF:

0.147

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0739

AC:

5020

AN:

67926

Other (OTH)

AF:

0.179

AC:

379

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

903

1806

2708

3611

4514

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.119

Hom.:

4950

Bravo

AF:

0.250

Asia WGS

AF:

0.132

AC:

460

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.026

(source)

DANN

Benign

0.27

PhyloP100

-1.6

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