rs11600

Positions:

• chr10-29422011-C-T

Variant summary

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

The ENST00000427063.8(SVIL-AS1):​n.1702C>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 0.0953 in 154,352 control chromosomes in the GnomAD database, including 888 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 0.095 (868 hom., cov: 32)
  • Exomes 𝑓: 0.12 (20 hom.)
• Consequence: SVIL-AS1 ENST00000427063.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

Genes affected

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

PTCHD3P1 (HGNC:44945): (patched domain containing 3 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SVIL-AS1	NR_110927.1	n.181+6599C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCHD3P1	ENST00000612350.1	n.2G>A		non_coding_transcript_exon_variant	1/1
SVIL-AS1	ENST00000684815.1	n.236+6599C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0950 AC: 14442 AN: 152016 Hom.: 869 Cov.: 32

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0870

GnomAD4 exome AF: 0.119 AC: 264 AN: 2218 Hom.: 20 Cov.: 0 AF XY: 0.117 AC XY: 143 AN XY: 1226

Gnomad4 AFR exome AF: 0.104

Gnomad4 AMR exome AF: 0.0208

Gnomad4 ASJ exome AF: 0.0625

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0391

Gnomad4 FIN exome AF: 0.162

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.116

GnomAD4 genome AF: 0.0949 AC: 14440 AN: 152134 Hom.: 868 Cov.: 32 AF XY: 0.0956 AC XY: 7112 AN XY: 74362

Gnomad4 AFR AF: 0.0464

Gnomad4 AMR AF: 0.0849

Gnomad4 ASJ AF: 0.0504

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0293

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.0861

Alfa AF: 0.109 Hom.: 272

Bravo AF: 0.0881

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11600; hg19: chr10-29710940;