dbSNP rs3741571: FZD10-AS1:n.2276G>A (chr12-130152232-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.466

Publications

4 publications found

Variant links:

Genes affected

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

FZD10-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FZD10-AS1	NR_033834.1 link	n.3039G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FZD10-AS1	ENST00000505807.6 link	n.2276G>A		non_coding_transcript_exon_variant	Exon 4 of 4	2
FZD10-AS1	ENST00000509760.1 link	n.3039G>A		non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.0425

AC:

6462

AN:

152166

Hom.:

204

Cov.:

show subpopulations

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:

AN:

146

Hom.:

Cov.:

AF XY:

0.0417

AC XY:

AN XY:

120

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0484

AC:

AN:

124

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0424

AC:

6461

AN:

152284

Hom.:

204

Cov.:

AF XY:

0.0425

AC XY:

3165

AN XY:

74452

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0559

AC:

3803

AN:

68018

Other (OTH)

AF:

0.0331

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

325

651

976

1302

1627

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.0

(source)

DANN

Benign

0.41

PhyloP100

-0.47

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over