12-53299619-C-G

Position:

• chr12-53299619-C-G

Variant summary

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

The ENST00000676527.1(ENSG00000288663):​n.737C>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 0.393 in 892,408 control chromosomes in the GnomAD database, including 71,848 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 0.35 (10128 hom., cov: 32)
  • Exomes 𝑓: 0.40 (61720 hom.)
• Consequence: ENSG00000288663 ENST00000676527.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

ENSG00000288663 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53299619C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288663	ENST00000676527.1	n.737C>G		non_coding_transcript_exon_variant	5/10
ENSG00000288663	ENST00000676632.1	n.1084C>G		non_coding_transcript_exon_variant	5/11
ENSG00000288663	ENST00000676940.1	n.782C>G		non_coding_transcript_exon_variant	6/12

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53662 AN: 151790 Hom.: 10113 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.401 AC: 296987 AN: 740498 Hom.: 61720 Cov.: 10 AF XY: 0.407 AC XY: 154129 AN XY: 378500

Gnomad4 AFR exome AF: 0.233

Gnomad4 AMR exome AF: 0.468

Gnomad4 ASJ exome AF: 0.407

Gnomad4 EAS exome AF: 0.596

Gnomad4 SAS exome AF: 0.535

Gnomad4 FIN exome AF: 0.377

Gnomad4 NFE exome AF: 0.378

Gnomad4 OTH exome AF: 0.397

GnomAD4 genome AF: 0.354 AC: 53708 AN: 151910 Hom.: 10128 Cov.: 32 AF XY: 0.356 AC XY: 26436 AN XY: 74244

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.377

Alfa AF: 0.241 Hom.: 606

Bravo AF: 0.351

Asia WGS AF: 0.544 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1465073; hg19: chr12-53693403;