rs7307229

Positions:

• chr12-6534437-C-G

Variant summary

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

The 12-6534437-C-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 320,268 control chromosomes in the GnomAD database, including 1,079 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 0.067 (1009 hom., cov: 33)
  • Exomes 𝑓: 0.012 (70 hom.)
• Consequence: GAPDH-DT XR_002957397.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

GAPDH-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAPDH-DT	XR_002957397.2			upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10099 AN: 151936 Hom.: 999 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0303

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.000974

Gnomad SAS AF: 0.0451

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00284

Gnomad OTH AF: 0.0468

GnomAD4 exome AF: 0.0124 AC: 2085 AN: 168206 Hom.: 70 Cov.: 0 AF XY: 0.0162 AC XY: 1515 AN XY: 93740

Gnomad4 AFR exome AF: 0.144

Gnomad4 AMR exome AF: 0.0124

Gnomad4 ASJ exome AF: 0.00884

Gnomad4 EAS exome AF: 0.000260

Gnomad4 SAS exome AF: 0.0400

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00205

Gnomad4 OTH exome AF: 0.0140

GnomAD4 genome AF: 0.0667 AC: 10146 AN: 152062 Hom.: 1009 Cov.: 33 AF XY: 0.0655 AC XY: 4869 AN XY: 74354

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0303

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.000976

Gnomad4 SAS AF: 0.0451

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00284

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0514 Hom.: 70

Bravo AF: 0.0748

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.36
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs7307229; hg19: chr12-6643603;