rs12314721

Positions:

• chr12-121127954-C-T

Variant summary

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

The variant allele was found at a frequency of 0.105 in 152,110 control chromosomes in the GnomAD database, including 883 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 0.10 (883 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.121127954C>T		intergenic_region
LOC105370032	XR_001749352.3	n.328-1113G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15934 AN: 151992 Hom.: 879 Cov.: 31

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0705

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0816

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.115

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.105 AC: 15951 AN: 152110 Hom.: 883 Cov.: 31 AF XY: 0.103 AC XY: 7653 AN XY: 74372

Gnomad4 AFR AF: 0.0946

Gnomad4 AMR AF: 0.0973

Gnomad4 ASJ AF: 0.0705

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0816

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.113

Alfa AF: 0.110 Hom.: 929

Bravo AF: 0.103

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12314721; hg19: chr12-121565757;