12-130146390-T-C

Variant names:

• chr12-130146390-T-C
• rs11060736
• ENST00000505807.6:n.8118A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505807.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FZD10-AS1	ENST00000505807.6	TSL:2	n.8118A>G		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0167 AC: 1 AN: 60

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0162 AC: 674 AN: 41564

American (AMR) AF: 0.102 AC: 1558 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3466

East Asian (EAS) AF: 0.206 AC: 1067 AN: 5168

South Asian (SAS) AF: 0.126 AC: 606 AN: 4824

European-Finnish (FIN) AF: 0.0959 AC: 1018 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0580 AC: 3946 AN: 68018

Other (OTH) AF: 0.0629 AC: 133 AN: 2116

Alfa AF: 0.0560 Hom.: 278

Bravo AF: 0.0580

Asia WGS AF: 0.142 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.59
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11060736; hg19: chr12-130630935;