chr2-6001154-T-C

Variant names:

• chr2-6001154-T-C
• rs941009
• ENST00000450794.4:n.932T>C

Variant summary

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

The ENST00000450794.4(SILC1):​n.932T>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 ENST00000450794.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 5 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=-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SILC1	ENST00000450794.4	n.932T>C		non_coding_transcript_exon_variant	Exon 3 of 3	4
SILC1	ENST00000654655.1	n.1272T>C		non_coding_transcript_exon_variant	Exon 6 of 6
SILC1	ENST00000660066.2	n.570T>C		non_coding_transcript_exon_variant	Exon 4 of 4

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

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.690 AC: 28610 AN: 41444

American (AMR) AF: 0.350 AC: 5340 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1965 AN: 5170

South Asian (SAS) AF: 0.359 AC: 1733 AN: 4826

European-Finnish (FIN) AF: 0.234 AC: 2471 AN: 10566

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15763 AN: 68000

Other (OTH) AF: 0.367 AC: 776 AN: 2114

Alfa AF: 0.291 Hom.: 24454

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs941009; hg19: chr2-6141286;