rs3741571

Variant names:

• chr12-130152232-C-T
• rs3741571
• ENST00000505807.6:n.2276G>A

Variant summary

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

The ENST00000505807.6(FZD10-AS1):​n.2276G>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 ENST00000505807.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.055 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FZD10-AS1	NR_033834.1		n.3039G>A		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FZD10-AS1	ENST00000505807.6	TSL:2	n.2276G>A		non_coding_transcript_exon	Exon 4 of 4
	FZD10-AS1	ENST00000509760.1	TSL:2	n.3039G>A		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.00 AC: 0 AN: 2

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

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0484 AC: 6 AN: 124

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.0145 AC: 601 AN: 41588

American (AMR) AF: 0.0243 AC: 371 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3470

East Asian (EAS) AF: 0.0456 AC: 235 AN: 5156

South Asian (SAS) AF: 0.0607 AC: 293 AN: 4824

European-Finnish (FIN) AF: 0.0781 AC: 829 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0559 AC: 3803 AN: 68018

Other (OTH) AF: 0.0331 AC: 70 AN: 2114

Alfa AF: 0.0499 Hom.: 371

Bravo AF: 0.0367

Asia WGS AF: 0.0430 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.41
PhyloP100		-0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3741571;

hg19: chr12-130636777;