Genetic Variant ENST00000414314.2:n.138-5801T>G (chr5-142458169-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.138-5801T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 152,290 control chromosomes in the GnomAD database, including 1,064 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 0.082 ( 1064 hom., cov: 33)

Consequence

SPRY4-AS1
ENST00000414314.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.150

Publications

0 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPRY4-AS1	NR_120664.1 link	n.507-5801T>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SPRY4-AS1	ENST00000414314.2 link	n.138-5801T>G	intron_variant	Intron 1 of 3	3
SPRY4-AS1	ENST00000425963.1 link	n.137-5801T>G	intron_variant	Intron 1 of 2	3
SPRY4-AS1	ENST00000443800.5 link	n.154-5801T>G	intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.0814

AC:

12389

AN:

152172

Hom.:

1065

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0514

Gnomad ASJ

AF:

0.00950

Gnomad EAS

AF:

0.0250

Gnomad SAS

AF:

0.0555

Gnomad FIN

AF:

0.0274

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0218

Gnomad OTH

AF:

0.0645

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

GnomAD4 genome

AF:

0.0815

AC:

12413

AN:

152290

Hom.:

1064

Cov.:

AF XY:

0.0801

AC XY:

5970

AN XY:

74486

show subpopulations

African (AFR)

AF:

0.224

AC:

9287

AN:

41524

American (AMR)

AF:

0.0512

AC:

784

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00950

AC:

AN:

3472

East Asian (EAS)

AF:

0.0249

AC:

129

AN:

5188

South Asian (SAS)

AF:

0.0553

AC:

267

AN:

4828

European-Finnish (FIN)

AF:

0.0274

AC:

291

AN:

10626

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0218

AC:

1480

AN:

68026

Other (OTH)

AF:

0.0638

AC:

135

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

539

1077

1616

2154

2693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<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:

0.0531

Hom.:

Bravo

AF:

0.0883

Asia WGS

AF:

0.0450

AC:

155

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.6

(source)

DANN

Benign

0.77

PhyloP100

-0.15

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