rs12427050

Variant names:

• chr12-97152614-G-A
• rs12427050
• ENST00000624902.1:n.2014C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-97152614-G-A
• chr12-97152614-G-T

Variant summary

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

The ENST00000624902.1(ENSG00000279190):​n.2014C>T 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 0.423 in 151,980 control chromosomes in the GnomAD database, including 14,761 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 0.42 (14761 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000279190 ENST00000624902.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

Genes affected

ENSG00000279190 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.622 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
ENSG00000279190	ENST00000624902.1	n.2014C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000258131	ENST00000552238.1	n.40-32462G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64296 AN: 151862 Hom.: 14746 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.456

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.423 AC: 64357 AN: 151980 Hom.: 14761 Cov.: 32 AF XY: 0.430 AC XY: 31946 AN XY: 74280

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.457

Alfa AF: 0.460 Hom.: 28193

Bravo AF: 0.425

Asia WGS AF: 0.601 AC: 2090 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	1.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12427050; hg19: chr12-97546392;