rs7159323

Positions:

• chr14-92923058-A-C
• chr14-92923058-A-G
• chr14-92923058-A-T

Variant summary

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

The XM_011536370.3(CHGA):​c.-189+46A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 258,476 control chromosomes in the GnomAD database, including 83,081 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 0.81 (49990 hom., cov: 33)
  • Exomes 𝑓: 0.79 (33091 hom.)
• Consequence: CHGA XM_011536370.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

Genes affected

CHGA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHGA	XM_011536370.3	c.-189+46A>C		intron_variant			XP_011534672.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122819 AN: 152084 Hom.: 49957 Cov.: 33

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.807

GnomAD4 exome AF: 0.787 AC: 83642 AN: 106274 Hom.: 33091 Cov.: 2 AF XY: 0.785 AC XY: 42685 AN XY: 54410

Gnomad4 AFR exome AF: 0.887

Gnomad4 AMR exome AF: 0.807

Gnomad4 ASJ exome AF: 0.751

Gnomad4 EAS exome AF: 0.955

Gnomad4 SAS exome AF: 0.827

Gnomad4 FIN exome AF: 0.734

Gnomad4 NFE exome AF: 0.766

Gnomad4 OTH exome AF: 0.794

GnomAD4 genome AF: 0.808 AC: 122909 AN: 152202 Hom.: 49990 Cov.: 33 AF XY: 0.807 AC XY: 60030 AN XY: 74406

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.809

Alfa AF: 0.682 Hom.: 1907

Bravo AF: 0.814

Asia WGS AF: 0.893 AC: 3106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	11
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7159323; hg19: chr14-93389403;