rs2609101

Variant names:

• chr2-6045502-A-C
• rs2609101
• ENST00000747556.1:n.603+5673A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-6045502-A-C
• chr2-6045502-A-T

Variant summary

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

The ENST00000747556.1(SILC1):​n.603+5673A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,904 control chromosomes in the GnomAD database, including 13,053 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 0.35 (13053 hom., cov: 32)
• Consequence: SILC1 ENST00000747556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747556.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SILC1	ENST00000747556.1		n.603+5673A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53216 AN: 151786 Hom.: 13007 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.351 AC: 53315 AN: 151904 Hom.: 13053 Cov.: 32 AF XY: 0.348 AC XY: 25832 AN XY: 74250

African (AFR) AF: 0.701 AC: 29019 AN: 41374

American (AMR) AF: 0.211 AC: 3229 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1073 AN: 5126

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4814

European-Finnish (FIN) AF: 0.256 AC: 2701 AN: 10566

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14340 AN: 67966

Other (OTH) AF: 0.329 AC: 694 AN: 2112

Alfa AF: 0.248 Hom.: 16809

Bravo AF: 0.364

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.43
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2609101; hg19: chr2-6185634;