rs3741571

chr12-130152232-C-T

Variant summary

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

The NR_033834.1(FZD10-AS1):n.3039G>A 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 0.0424 in 152,430 control chromosomes in the GnomAD database, including 204 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 0.042 (204 hom., cov: 34)
  • Exomes 𝑓: 0.041 (0 hom.)
• Consequence: FZD10-AS1 NR_033834.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466

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 (SAS) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FZD10-AS1	NR_033834.1	n.3039G>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FZD10-AS1	ENST00000505807.6	n.2276G>A		non_coding_transcript_exon_variant	4/4	2
FZD10-AS1	ENST00000509760.1	n.3039G>A		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.0425 AC: 6462 AN: 152166 Hom.: 204 Cov.: 34

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0243

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.0335

GnomAD4 exome AF: 0.0411 AC: 6 AN: 146 Hom.: 0 Cov.: 0 AF XY: 0.0417 AC XY: 5 AN XY: 120

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0484

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0424 AC: 6461 AN: 152284 Hom.: 204 Cov.: 34 AF XY: 0.0425 AC XY: 3165 AN XY: 74452

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0243

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.0456

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.0559

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0515 Hom.: 301

Bravo AF: 0.0367

Asia WGS AF: 0.0430 AC: 148 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	2.0
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3741571; hg19: chr12-130636777;