chr12-6534150-T-C

Position:

• chr12-6534150-T-C

Variant summary

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

The XR_002957397.2(GAPDH-DT):​n.258A>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 0.274 in 153,780 control chromosomes in the GnomAD database, including 6,356 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 0.27 (6309 hom., cov: 33)
  • Exomes 𝑓: 0.19 (47 hom.)
• Consequence: GAPDH-DT XR_002957397.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242

Genes affected

GAPDH-DT (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 = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAPDH-DT	XR_002957397.2	n.258A>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41717 AN: 151934 Hom.: 6293 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.236

GnomAD4 exome AF: 0.192 AC: 332 AN: 1728 Hom.: 47 Cov.: 0 AF XY: 0.201 AC XY: 230 AN XY: 1144

Gnomad4 AFR exome AF: 0.286

Gnomad4 AMR exome AF: 0.196

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.375

Gnomad4 SAS exome AF: 0.190

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.188

Gnomad4 OTH exome AF: 0.233

GnomAD4 genome AF: 0.275 AC: 41776 AN: 152052 Hom.: 6309 Cov.: 33 AF XY: 0.278 AC XY: 20637 AN XY: 74350

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.240

Alfa AF: 0.217 Hom.: 6699

Bravo AF: 0.280

Asia WGS AF: 0.381 AC: 1323 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	8.6
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6489721; hg19: chr12-6643316;