rs11007559

Positions:

• chr10-29409357-C-A

Variant summary

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

The ENST00000658254.1(ENSG00000287402):​n.10G>T 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 0.211 in 153,506 control chromosomes in the GnomAD database, including 3,589 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 0.21 (3556 hom., cov: 33)
  • Exomes 𝑓: 0.19 (33 hom.)
• Consequence: ENST00000658254.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

Genes affected

(HGNC:):

SVIL-AS1 (HGNC:51219): (SVIL antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376474	XR_930787.3	n.97G>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658254.1	n.10G>T		non_coding_transcript_exon_variant	1/3
SVIL-AS1	ENST00000430295.5			upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32071 AN: 152078 Hom.: 3556 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.195 AC: 255 AN: 1308 Hom.: 33 Cov.: 0 AF XY: 0.178 AC XY: 128 AN XY: 718

Gnomad4 AFR exome AF: 0.188

Gnomad4 AMR exome AF: 0.130

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.0877

Gnomad4 SAS exome AF: 0.0769

Gnomad4 FIN exome AF: 0.296

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.221

GnomAD4 genome AF: 0.211 AC: 32094 AN: 152198 Hom.: 3556 Cov.: 33 AF XY: 0.210 AC XY: 15622 AN XY: 74402

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0382

Gnomad4 SAS AF: 0.0951

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.211

Alfa AF: 0.205 Hom.: 5297

Bravo AF: 0.211

Asia WGS AF: 0.0730 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11007559; hg19: chr10-29698286;