12-120398546-T-A

Variant names:

• chr12-120398546-T-A
• rs206970

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.403 AC: 16680 AN: 41412

American (AMR) AF: 0.257 AC: 3909 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1305 AN: 5154

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4816

European-Finnish (FIN) AF: 0.252 AC: 2658 AN: 10554

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14358 AN: 67978

Other (OTH) AF: 0.255 AC: 536 AN: 2106

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs206970; hg19: chr12-120836349;