Genetic Variant SPRY4-AS1:n.867C>T (chr5-142533276-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 ENST00000668207.1(SPRY4-AS1):n.867C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,054 control chromosomes in the GnomAD database, including 3,828 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 ( 3828 hom., cov: 33)

Consequence

SPRY4-AS1
ENST00000668207.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.104

Publications

3 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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	ENST00000668207.1 link	n.867C>T	non_coding_transcript_exon_variant	Exon 5 of 5
SPRY4-AS1	ENST00000414314.2 link	n.228-48526C>T	intron_variant	Intron 2 of 3	3
SPRY4-AS1	ENST00000443800.5 link	n.244-48526C>T	intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31668

AN:

151936

Hom.:

3821

Cov.:

show subpopulations

Gnomad AFR

AF:

0.279

Gnomad AMI

AF:

0.178

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.181

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

GnomAD4 genome

AF:

0.208

AC:

31698

AN:

152054

Hom.:

3828

Cov.:

AF XY:

0.213

AC XY:

15847

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.279

AC:

11571

AN:

41432

American (AMR)

AF:

0.192

AC:

2936

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

801

AN:

3468

East Asian (EAS)

AF:

0.495

AC:

2562

AN:

5174

South Asian (SAS)

AF:

0.286

AC:

1377

AN:

4820

European-Finnish (FIN)

AF:

0.178

AC:

1876

AN:

10568

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.147

AC:

9980

AN:

67988

Other (OTH)

AF:

0.183

AC:

387

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1277

2554

3831

5108

6385

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

336

672

1008

1344

1680

<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:

0.162

Hom.:

3679

Bravo

AF:

0.214

Asia WGS

AF:

0.352

AC:

1220

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.3

(source)

DANN

Benign

0.64

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