chr2-5980457-T-G

Variant names:

• chr2-5980457-T-G
• rs1880800
• ENST00000431188.1:n.297T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654672.2(SILC1):​n.825T>G 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 0.586 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 ENST00000654672.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654672.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SILC1	NR_026832.1		n.*239T>G		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SILC1	ENST00000431188.1	TSL:5	n.297T>G		non_coding_transcript_exon	Exon 3 of 5
	SILC1	ENST00000456327.1	TSL:5	n.1204T>G		non_coding_transcript_exon	Exon 5 of 5
	SILC1	ENST00000654672.2		n.825T>G		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.835 AC: 34668 AN: 41516

American (AMR) AF: 0.518 AC: 7918 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3470

East Asian (EAS) AF: 0.708 AC: 3658 AN: 5170

South Asian (SAS) AF: 0.628 AC: 3022 AN: 4814

European-Finnish (FIN) AF: 0.380 AC: 4010 AN: 10566

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32151 AN: 67972

Other (OTH) AF: 0.591 AC: 1247 AN: 2110

Alfa AF: 0.508 Hom.: 33954

Bravo AF: 0.607

Asia WGS AF: 0.647 AC: 2251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.6
DANN	Benign	0.78
PhyloP100		0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1880800;

hg19: chr2-6120589;