chr2-5984889-T-G

Variant names:

• chr2-5984889-T-G
• rs1079417
• ENST00000431188.1:n.3325T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444416.1(SILC1):​n.2687T>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 0.576 in 152,098 control chromosomes in the GnomAD database, including 25,265 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 0.58 (25265 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: SILC1 ENST00000444416.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

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

LOC400940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC400940	NR_026833.1	n.656-536T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SILC1	ENST00000431188.1	n.3325T>G		non_coding_transcript_exon_variant	Exon 5 of 5	5
SILC1	ENST00000444416.1	n.2687T>G		non_coding_transcript_exon_variant	Exon 2 of 2	2
SILC1	ENST00000431182.3	n.1415-536T>G		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87559 AN: 151980 Hom.: 25268 Cov.: 33

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.598

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.576 AC: 87593 AN: 152098 Hom.: 25265 Cov.: 33 AF XY: 0.576 AC XY: 42793 AN XY: 74344

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.594

Alfa AF: 0.572 Hom.: 40993

Bravo AF: 0.570

Asia WGS AF: 0.605 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1079417; hg19: chr2-6125021;