rs12427050

chr12-97152614-G-Achr12-97152614-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: ENST00000624902.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000624902.1	n.2014C>T		non_coding_transcript_exon_variant	1/1
	ENST00000552238.1	n.40-32462G>A		intron_variant, non_coding_transcript_variant		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;