2-5980457-T-G

Position:

• chr2-5980457-T-G

Variant summary

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

The ENST00000654655.1(SILC1):​n.889-2316T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,122 control chromosomes in the GnomAD database, including 28,315 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 0.59 (28314 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: SILC1 ENST00000654655.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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.889-2316T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89050 AN: 152002 Hom.: 28276 Cov.: 33

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.593

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.586 AC: 89128 AN: 152120 Hom.: 28314 Cov.: 33 AF XY: 0.582 AC XY: 43269 AN XY: 74358

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.591

Alfa AF: 0.498 Hom.: 25687

Bravo AF: 0.607

Asia WGS AF: 0.647 AC: 2251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880800; hg19: chr2-6120589;