chr10-29422011-C-T

Variant names:

• chr10-29422011-C-T
• rs11600
• ENST00000427063.9:n.1702C>T

Variant summary

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

The ENST00000427063.9(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 ENST00000427063.9 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 6 publications found

Genes affected

SVIL-AS1 (HGNC:):

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

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SVIL-AS1	NR_003930.2	n.1702C>T		non_coding_transcript_exon_variant	Exon 3 of 3
SVIL-AS1	NR_110923.1	n.1728C>T		non_coding_transcript_exon_variant	Exon 3 of 3
SVIL-AS1	NR_110924.1	n.1727C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SVIL-AS1	ENST00000427063.9	n.1702C>T		non_coding_transcript_exon_variant	Exon 3 of 3	1
SVIL-AS1	ENST00000623175.5	n.1734C>T		non_coding_transcript_exon_variant	Exon 3 of 3	1
SVIL-AS1	ENST00000413405.7	n.211+6599C>T		intron_variant	Intron 2 of 2	1

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

African (AFR) AF: 0.104 AC: 5 AN: 48

American (AMR) AF: 0.0208 AC: 1 AN: 48

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 2 AN: 32

East Asian (EAS) AF: 0.00 AC: 0 AN: 60

South Asian (SAS) AF: 0.0391 AC: 5 AN: 128

European-Finnish (FIN) AF: 0.162 AC: 84 AN: 520

Middle Eastern (MID) AF: 0.0511 AC: 9 AN: 176

European-Non Finnish (NFE) AF: 0.133 AC: 141 AN: 1060

Other (OTH) AF: 0.116 AC: 17 AN: 146

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

African (AFR) AF: 0.0464 AC: 1927 AN: 41506

American (AMR) AF: 0.0849 AC: 1298 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0504 AC: 175 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0293 AC: 141 AN: 4818

European-Finnish (FIN) AF: 0.146 AC: 1544 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 9004 AN: 67976

Other (OTH) AF: 0.0861 AC: 182 AN: 2114

Alfa AF: 0.108 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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs11600; hg19: chr10-29710940;