dbSNP rs4513773: SCIRT:n.520-25613T>C (chr6-43957789-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.520-25613T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,070 control chromosomes in the GnomAD database, including 14,850 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 0.44 ( 14850 hom., cov: 32)

Consequence

SCIRT
ENST00000687158.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.376

Publications

16 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=-0.75).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.528 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.520-25613T>C	intron_variant	Intron 3 of 3
SCIRT	ENST00000687455.2 link	n.245-25613T>C	intron_variant	Intron 2 of 2
SCIRT	ENST00000687843.1 link	n.593-25613T>C	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.438

AC:

66513

AN:

151952

Hom.:

14838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.600

Gnomad AMR

AF:

0.537

Gnomad ASJ

AF:

0.436

Gnomad EAS

AF:

0.310

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.479

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.463

Gnomad OTH

AF:

0.423

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

GnomAD4 genome

AF:

0.438

AC:

66539

AN:

152070

Hom.:

14850

Cov.:

AF XY:

0.438

AC XY:

32565

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.370

AC:

15338

AN:

41470

American (AMR)

AF:

0.537

AC:

8212

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.436

AC:

1511

AN:

3466

East Asian (EAS)

AF:

0.309

AC:

1602

AN:

5182

South Asian (SAS)

AF:

0.372

AC:

1790

AN:

4810

European-Finnish (FIN)

AF:

0.479

AC:

5057

AN:

10564

Middle Eastern (MID)

AF:

0.342

AC:

100

AN:

292

European-Non Finnish (NFE)

AF:

0.463

AC:

31489

AN:

67974

Other (OTH)

AF:

0.422

AC:

893

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1885

3770

5656

7541

9426

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<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:

0.0655

Hom.:

2618

Bravo

AF:

0.440

Asia WGS

AF:

0.344

AC:

1198

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.77

(source)

DANN

Benign

0.80

PhyloP100

-0.38

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