rs7315725

Positions:

• chr12-13194811-G-A

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 0.188 in 151,942 control chromosomes in the GnomAD database, including 2,976 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 0.19 (2976 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

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 (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.13194811G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28637 AN: 151826 Hom.: 2976 Cov.: 31

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.188 AC: 28638 AN: 151942 Hom.: 2976 Cov.: 31 AF XY: 0.190 AC XY: 14079 AN XY: 74282

Gnomad4 AFR AF: 0.0919

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.185

Alfa AF: 0.229 Hom.: 4122

Bravo AF: 0.176

Asia WGS AF: 0.221 AC: 768 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	2.4
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7315725; hg19: chr12-13347745;