rs12305135

Variant names:

• chr12-130150660-T-C
• rs12305135
• ENST00000505807.6:n.3848A>G

Variant summary

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

The ENST00000505807.6(FZD10-AS1):​n.3848A>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 0.071 in 152,324 control chromosomes in the GnomAD database, including 498 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 0.071 (498 hom., cov: 34)
  • Exomes 𝑓: 0.091 (0 hom.)
• Consequence: FZD10-AS1 ENST00000505807.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FZD10-AS1	ENST00000505807.6	n.3848A>G		non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.0709 AC: 10790 AN: 152184 Hom.: 500 Cov.: 34

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0673

GnomAD4 exome AF: 0.0909 AC: 2 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.111 AC XY: 2 AN XY: 18

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0710 AC: 10807 AN: 152302 Hom.: 498 Cov.: 34 AF XY: 0.0753 AC XY: 5609 AN XY: 74470

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.0979

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0737

Gnomad4 OTH AF: 0.0690

Alfa AF: 0.0386 Hom.: 28

Bravo AF: 0.0674

Asia WGS AF: 0.141 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12305135; hg19: chr12-130635205;