2-5944602-A-T

Variant names:

• chr2-5944602-A-T
• rs10495531
• ENST00000431182.3:n.201+11681A>T

Variant summary

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

The ENST00000431182.3(SILC1):​n.201+11681A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,130 control chromosomes in the GnomAD database, including 11,722 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 0.37 (11722 hom., cov: 33)
• Consequence: SILC1 ENST00000431182.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431182.3. 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
	SILC1	NR_026832.1		n.235+11681A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SILC1	ENST00000431182.3	TSL:4	n.201+11681A>T		intron	N/A
	SILC1	ENST00000431188.1	TSL:5	n.134+11681A>T		intron	N/A
	SILC1	ENST00000456327.1	TSL:5	n.235+11681A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56446 AN: 152012 Hom.: 11721 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.371 AC: 56448 AN: 152130 Hom.: 11722 Cov.: 33 AF XY: 0.373 AC XY: 27755 AN XY: 74358

African (AFR) AF: 0.191 AC: 7948 AN: 41520

American (AMR) AF: 0.316 AC: 4826 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1361 AN: 5170

South Asian (SAS) AF: 0.433 AC: 2092 AN: 4830

European-Finnish (FIN) AF: 0.568 AC: 5997 AN: 10558

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31200 AN: 67984

Other (OTH) AF: 0.366 AC: 774 AN: 2114

Alfa AF: 0.411 Hom.: 1696

Bravo AF: 0.339

Asia WGS AF: 0.334 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.40
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10495531; hg19: chr2-6084734;