12-38912965-G-A

Position:

• chr12-38912965-G-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 0.0406 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0406 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

Gnomad4 AFR AF: 0.0111

Gnomad4 AMR AF: 0.0317

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.0828

Gnomad4 SAS AF: 0.0644

Gnomad4 FIN AF: 0.0348

Gnomad4 NFE AF: 0.0564

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0511 Hom.: 121

Bravo AF: 0.0386

Asia WGS AF: 0.0810 AC: 280 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12423647; hg19: chr12-39306767;