rs1405262

Variant names:

• chr2-5994808-T-C
• rs1405262
• ENST00000665790.1:n.1588T>C

Variant summary

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

The ENST00000665790.1(SILC1):​n.1588T>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 0.116 in 152,236 control chromosomes in the GnomAD database, including 1,452 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 0.12 (1452 hom., cov: 32)
• Consequence: SILC1 ENST00000665790.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SILC1	ENST00000665790.1	n.1588T>C		non_coding_transcript_exon_variant	Exon 4 of 4
SILC1	ENST00000450794.4	n.761-6175T>C		intron_variant	Intron 2 of 2	4
SILC1	ENST00000654655.1	n.1100+603T>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17678 AN: 152120 Hom.: 1452 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0944

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.116 AC: 17691 AN: 152236 Hom.: 1452 Cov.: 32 AF XY: 0.124 AC XY: 9235 AN XY: 74420

African (AFR) AF: 0.149 AC: 6203 AN: 41554

American (AMR) AF: 0.110 AC: 1679 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0944 AC: 327 AN: 3464

East Asian (EAS) AF: 0.374 AC: 1928 AN: 5156

South Asian (SAS) AF: 0.259 AC: 1249 AN: 4818

European-Finnish (FIN) AF: 0.168 AC: 1780 AN: 10598

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0616 AC: 4188 AN: 68030

Other (OTH) AF: 0.109 AC: 231 AN: 2114

Alfa AF: 0.0840 Hom.: 3459

Bravo AF: 0.112

Asia WGS AF: 0.270 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.0
DANN	Benign	0.39
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs1405262; hg19: chr2-6134940;