rs1399236

Positions:

• chr12-101210444-T-C

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 0.159 in 152,350 control chromosomes in the GnomAD database, including 2,069 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 0.16 (2063 hom., cov: 32)
  • Exomes 𝑓: 0.18 (6 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101210444T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24118 AN: 152058 Hom.: 2063 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0644

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.178

GnomAD4 exome AF: 0.184 AC: 32 AN: 174 Hom.: 6 Cov.: 0 AF XY: 0.185 AC XY: 17 AN XY: 92

Gnomad4 AFR exome AF: 0.300

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.0625

Gnomad4 NFE exome AF: 0.169

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.159 AC: 24141 AN: 152176 Hom.: 2063 Cov.: 32 AF XY: 0.160 AC XY: 11887 AN XY: 74402

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0647

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.178

Alfa AF: 0.164 Hom.: 2347

Bravo AF: 0.164

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.54
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1399236; hg19: chr12-101604222;