Genetic Variant SILC1:n.201+11681A>T (chr2-5944602-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000431182.3(SILC1):n.201+11681A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,130 control chromosomes in the GnomAD database, including 11,722 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 0.37 ( 11722 hom., cov: 33)

Consequence

SILC1
ENST00000431182.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.542

Publications

3 publications found

Variant links:

Genes affected

SILC1 (HGNC:26403): (sciatic injury induced lincRNA upregulator of SOX11)

SILC1 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SILC1	NR_026832.1 link	n.235+11681A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SILC1	ENST00000431182.3 link	n.201+11681A>T	intron_variant	Intron 1 of 3	4
SILC1	ENST00000431188.1 link	n.134+11681A>T	intron_variant	Intron 1 of 4	5
SILC1	ENST00000456327.1 link	n.235+11681A>T	intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56446

AN:

152012

Hom.:

11721

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.316

Gnomad ASJ

AF:

0.486

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.433

Gnomad FIN

AF:

0.568

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.367

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

GnomAD4 genome

AF:

0.371

AC:

56448

AN:

152130

Hom.:

11722

Cov.:

AF XY:

0.373

AC XY:

27755

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.191

AC:

7948

AN:

41520

American (AMR)

AF:

0.316

AC:

4826

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.486

AC:

1685

AN:

3468

East Asian (EAS)

AF:

0.263

AC:

1361

AN:

5170

South Asian (SAS)

AF:

0.433

AC:

2092

AN:

4830

European-Finnish (FIN)

AF:

0.568

AC:

5997

AN:

10558

Middle Eastern (MID)

AF:

0.418

AC:

123

AN:

294

European-Non Finnish (NFE)

AF:

0.459

AC:

31200

AN:

67984

Other (OTH)

AF:

0.366

AC:

774

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1722

3444

5166

6888

8610

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

550

1100

1650

2200

2750

<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:

0.411

Hom.:

1696

Bravo

AF:

0.339

Asia WGS

AF:

0.334

AC:

1163

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.28

(source)

DANN

Benign

0.40

PhyloP100

-0.54

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