chr12-53936191-T-C

Position:

• chr12-53936191-T-C

Variant summary

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

The NR_047507.1(HOXC13-AS):​n.545A>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 0.59 in 152,014 control chromosomes in the GnomAD database, including 28,727 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 0.59 (28714 hom., cov: 31)
  • Exomes 𝑓: 0.71 (13 hom.)
• Consequence: HOXC13-AS NR_047507.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

HOXC13-AS (HGNC:43753): (HOXC13 antisense RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HOXC13-AS	NR_047507.1	n.545A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HOXC13-AS	ENST00000512916.2	n.545A>G		non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89603 AN: 151846 Hom.: 28713 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.603

GnomAD4 exome AF: 0.708 AC: 34 AN: 48 Hom.: 13 Cov.: 0 AF XY: 0.789 AC XY: 30 AN XY: 38

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.725

GnomAD4 genome AF: 0.590 AC: 89611 AN: 151966 Hom.: 28714 Cov.: 31 AF XY: 0.592 AC XY: 43949 AN XY: 74270

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.597

Alfa AF: 0.673 Hom.: 55421

Bravo AF: 0.588

Asia WGS AF: 0.538 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1867299; hg19: chr12-54329975;