Genetic Variant SCIRT:n.519+28024T>C (chr6-43971194-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000687158.2(SCIRT):n.519+28024T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,018 control chromosomes in the GnomAD database, including 22,664 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 0.53 ( 22664 hom., cov: 32)

Consequence

SCIRT
ENST00000687158.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.313

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
SCIRT	ENST00000687158.2 link	n.519+28024T>C	intron_variant	Intron 3 of 3
SCIRT	ENST00000687455.2 link	n.244+29849T>C	intron_variant	Intron 2 of 2
SCIRT	ENST00000687843.1 link	n.592+28024T>C	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80361

AN:

151900

Hom.:

22608

Cov.:

show subpopulations

Gnomad AFR

AF:

0.681

Gnomad AMI

AF:

0.444

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.0994

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.535

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.506

Gnomad OTH

AF:

0.500

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

GnomAD4 genome

AF:

0.529

AC:

80476

AN:

152018

Hom.:

22664

Cov.:

AF XY:

0.520

AC XY:

38620

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.681

AC:

28260

AN:

41468

American (AMR)

AF:

0.491

AC:

7494

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.380

AC:

1320

AN:

3470

East Asian (EAS)

AF:

0.0992

AC:

513

AN:

5170

South Asian (SAS)

AF:

0.264

AC:

1271

AN:

4820

European-Finnish (FIN)

AF:

0.535

AC:

5670

AN:

10592

Middle Eastern (MID)

AF:

0.395

AC:

116

AN:

294

European-Non Finnish (NFE)

AF:

0.506

AC:

34382

AN:

67918

Other (OTH)

AF:

0.496

AC:

1047

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1846

3691

5537

7382

9228

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

670

1340

2010

2680

3350

<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:

0.541

Hom.:

3740

Bravo

AF:

0.540

Asia WGS

AF:

0.233

AC:

811

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.2

(source)

DANN

Benign

0.48

PhyloP100

-0.31

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