12-133077993-C-T

Position:

• chr12-133077993-C-T

Variant summary

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

The ENST00000624401.1(ENSG00000279817):​n.400G>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 0.435 in 152,004 control chromosomes in the GnomAD database, including 15,986 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 0.43 (15986 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENST00000624401.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000624401.1	n.400G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66025 AN: 151878 Hom.: 15980 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.501

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.435 AC: 66049 AN: 151996 Hom.: 15986 Cov.: 32 AF XY: 0.441 AC XY: 32742 AN XY: 74284

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.503

Alfa AF: 0.470 Hom.: 8736

Bravo AF: 0.439

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs595241; hg19: chr12-133654579;