12-38912965-G-A

Variant names:

• chr12-38912965-G-A
• rs12423647

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 0.0406 in 152,190 control chromosomes in the GnomAD database, including 143 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 0.041 (143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.0763 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: 0.0406 AC: 6176 AN: 152074 Hom.: 143 Cov.: 32

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.0826

Gnomad SAS AF: 0.0637

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0406 AC: 6176 AN: 152190 Hom.: 143 Cov.: 32 AF XY: 0.0404 AC XY: 3003 AN XY: 74404

African (AFR) AF: 0.0111 AC: 460 AN: 41528

American (AMR) AF: 0.0317 AC: 485 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 157 AN: 3472

East Asian (EAS) AF: 0.0828 AC: 429 AN: 5182

South Asian (SAS) AF: 0.0644 AC: 310 AN: 4814

European-Finnish (FIN) AF: 0.0348 AC: 369 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0564 AC: 3837 AN: 67998

Other (OTH) AF: 0.0449 AC: 95 AN: 2114

Alfa AF: 0.0510 Hom.: 132

Bravo AF: 0.0386

Asia WGS AF: 0.0810 AC: 280 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.24
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs12423647; hg19: chr12-39306767;