rs206970

chr12-120398546-T-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 0.274 in 151,932 control chromosomes in the GnomAD database, including 6,292 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 0.27 (6292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41679 AN: 151814 Hom.: 6288 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.274 AC: 41702 AN: 151932 Hom.: 6292 Cov.: 31 AF XY: 0.273 AC XY: 20286 AN XY: 74268

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.255

Alfa AF: 0.243 Hom.: 618

Bravo AF: 0.282

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.18
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs206970; hg19: chr12-120836349;