12-56104457-G-A

Position:

• chr12-56104457-G-A

Variant summary

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

The 12-56104457-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 656,956 control chromosomes in the GnomAD database, including 3,852 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 0.12 (1138 hom., cov: 32)
  • Exomes 𝑓: 0.097 (2714 hom.)
• Consequence: LOC105369782 XR_944995.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

LOC105369782 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369782	XR_944995.4			upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17602 AN: 152118 Hom.: 1133 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0880

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0966

GnomAD4 exome AF: 0.0972 AC: 49082 AN: 504720 Hom.: 2714 Cov.: 0 AF XY: 0.0961 AC XY: 26354 AN XY: 274300

Gnomad4 AFR exome AF: 0.158

Gnomad4 AMR exome AF: 0.0601

Gnomad4 ASJ exome AF: 0.107

Gnomad4 EAS exome AF: 0.000387

Gnomad4 SAS exome AF: 0.0788

Gnomad4 FIN exome AF: 0.118

Gnomad4 NFE exome AF: 0.109

Gnomad4 OTH exome AF: 0.103

GnomAD4 genome AF: 0.116 AC: 17621 AN: 152236 Hom.: 1138 Cov.: 32 AF XY: 0.115 AC XY: 8571 AN XY: 74442

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0760

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0956

Alfa AF: 0.108 Hom.: 905

Bravo AF: 0.114

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	15
DANN	Benign	0.82

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: rs773121; hg19: chr12-56498241;