dbSNP rs9381282: SCIRT:n.156+33909G>T (chr6-44040588-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000422059.5(SCIRT):n.156+33909G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,142 control chromosomes in the GnomAD database, including 3,227 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 0.18 ( 3227 hom., cov: 32)

Consequence

SCIRT
ENST00000422059.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.111

Publications

5 publications found

Variant links:

Genes affected

SCIRT (HGNC:55341): (stem cell inhibitory RNA transcript)

SCIRT 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCIRT	NR_125864.1 link	n.156+33909G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SCIRT	ENST00000422059.5 link	n.156+33909G>T	intron_variant	Intron 1 of 4	2
SCIRT	ENST00000652850.2 link	n.154+33909G>T	intron_variant	Intron 1 of 3
SCIRT	ENST00000687158.2 link	n.154+33909G>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27359

AN:

152024

Hom.:

3222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0645

Gnomad AMI

AF:

0.254

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.540

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.180

AC:

27375

AN:

152142

Hom.:

3227

Cov.:

AF XY:

0.187

AC XY:

13908

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.0643

AC:

2671

AN:

41542

American (AMR)

AF:

0.229

AC:

3505

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

716

AN:

3470

East Asian (EAS)

AF:

0.540

AC:

2780

AN:

5152

South Asian (SAS)

AF:

0.381

AC:

1830

AN:

4804

European-Finnish (FIN)

AF:

0.211

AC:

2237

AN:

10592

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.191

AC:

12950

AN:

67970

Other (OTH)

AF:

0.191

AC:

403

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1079

2159

3238

4318

5397

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<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:

0.192

Hom.:

12363

Bravo

AF:

0.175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.1

(source)

DANN

Benign

0.37

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