rs11060736

chr12-130146390-T-C

Variant summary

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

The ENST00000505807.6(FZD10-AS1):n.8118A>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 0.0603 in 152,340 control chromosomes in the GnomAD database, including 419 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 0.060 (419 hom., cov: 33)
  • Exomes 𝑓: 0.015 (0 hom.)
• Consequence: FZD10-AS1 ENST00000505807.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

Genes affected

FZD10-AS1 (HGNC:48632): (FZD10 antisense divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FZD10-AS1	ENST00000505807.6	n.8118A>G		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9180 AN: 152154 Hom.: 421 Cov.: 33

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.0611

GnomAD4 exome AF: 0.0147 AC: 1 AN: 68 Hom.: 0 Cov.: 0 AF XY: 0.0192 AC XY: 1 AN XY: 52

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 NFE exome AF: 0.0167

GnomAD4 genome AF: 0.0603 AC: 9183 AN: 152272 Hom.: 419 Cov.: 33 AF XY: 0.0655 AC XY: 4876 AN XY: 74448

Gnomad4 AFR AF: 0.0162

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0959

Gnomad4 NFE AF: 0.0580

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0617 Hom.: 215

Bravo AF: 0.0580

Asia WGS AF: 0.142 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.5
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11060736; hg19: chr12-130630935;