rs12305135

Variant names:

• chr12-130150660-T-C
• rs12305135
• ENST00000505807.6:n.3848A>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.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
• Publications: 1 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 (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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

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

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.143 AC: 2 AN: 14

Other (OTH) AF: 0.00 AC: 0 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00233887), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.0280 AC: 1163 AN: 41578

American (AMR) AF: 0.0979 AC: 1499 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1031 AN: 5166

South Asian (SAS) AF: 0.124 AC: 600 AN: 4828

European-Finnish (FIN) AF: 0.107 AC: 1134 AN: 10618

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0737 AC: 5015 AN: 68014

Other (OTH) AF: 0.0690 AC: 146 AN: 2116

Alfa AF: 0.0491 Hom.: 110

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs12305135; hg19: chr12-130635205;