12-23486983-A-G

Variant names:

• chr12-23486983-A-G
• rs2120771

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 0.228 in 151,984 control chromosomes in the GnomAD database, including 4,792 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 0.23 (4792 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34556 AN: 151866 Hom.: 4787 Cov.: 31

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.228 AC: 34578 AN: 151984 Hom.: 4792 Cov.: 31 AF XY: 0.229 AC XY: 17010 AN XY: 74270

African (AFR) AF: 0.0861 AC: 3575 AN: 41504

American (AMR) AF: 0.281 AC: 4277 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1120 AN: 3462

East Asian (EAS) AF: 0.551 AC: 2845 AN: 5166

South Asian (SAS) AF: 0.338 AC: 1629 AN: 4816

European-Finnish (FIN) AF: 0.225 AC: 2369 AN: 10538

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17839 AN: 67942

Other (OTH) AF: 0.264 AC: 558 AN: 2110

Alfa AF: 0.255 Hom.: 18056

Bravo AF: 0.230

Asia WGS AF: 0.396 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.67
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2120771; hg19: chr12-23639917;