2-6029219-A-G

Variant names:

• chr2-6029219-A-G
• rs7571496
• ENST00000747556.1:n.308-5943A>G

Variant summary

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

The ENST00000747556.1(SILC1):​n.308-5943A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,884 control chromosomes in the GnomAD database, including 13,118 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 0.39 (13118 hom., cov: 32)
• Consequence: SILC1 ENST00000747556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• 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 (EAS) allele frequency at 95% confidence interval = 0.627 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SILC1	ENST00000747556.1		n.308-5943A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58990 AN: 151766 Hom.: 13088 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.389 AC: 59071 AN: 151884 Hom.: 13118 Cov.: 32 AF XY: 0.397 AC XY: 29445 AN XY: 74224

African (AFR) AF: 0.571 AC: 23638 AN: 41408

American (AMR) AF: 0.336 AC: 5126 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1157 AN: 3468

East Asian (EAS) AF: 0.645 AC: 3312 AN: 5136

South Asian (SAS) AF: 0.501 AC: 2406 AN: 4806

European-Finnish (FIN) AF: 0.399 AC: 4210 AN: 10556

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18080 AN: 67928

Other (OTH) AF: 0.376 AC: 792 AN: 2108

Alfa AF: 0.299 Hom.: 6615

Bravo AF: 0.389

Asia WGS AF: 0.577 AC: 2006 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	0.42
DANN	Benign	0.72
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7571496; hg19: chr2-6169351;