Genetic Variant 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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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