rs941009

chr2-6001154-T-Cchr2-6001154-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654655.1(SILC1):n.1272T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,064 control chromosomes in the GnomAD database, including 14,073 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 0.38 (14073 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SILC1 ENST00000654655.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SILC1	ENST00000654655.1	n.1272T>C		non_coding_transcript_exon_variant	6/6

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57908 AN: 151946 Hom.: 14044 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.370

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.381 AC: 57993 AN: 152064 Hom.: 14073 Cov.: 32 AF XY: 0.380 AC XY: 28246 AN XY: 74356

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.367

Alfa AF: 0.263 Hom.: 12075

Bravo AF: 0.405

Asia WGS AF: 0.371 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.23
Dann	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs941009; hg19: chr2-6141286;