12-97152614-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000279190 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624902.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279190	ENST00000624902.1	TSL:6	n.2014C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000257470	ENST00000716365.1		n.206-32575G>A		intron	N/A
	ENSG00000257470	ENST00000716366.1		n.185-32462G>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.256 AC: 10610 AN: 41446

American (AMR) AF: 0.579 AC: 8826 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3466

East Asian (EAS) AF: 0.587 AC: 3037 AN: 5176

South Asian (SAS) AF: 0.641 AC: 3090 AN: 4820

European-Finnish (FIN) AF: 0.423 AC: 4455 AN: 10538

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31482 AN: 67962

Other (OTH) AF: 0.457 AC: 967 AN: 2114

Alfa AF: 0.455 Hom.: 63389

Bravo AF: 0.425

Asia WGS AF: 0.601 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs12427050; hg19: chr12-97546392;