12-11925042-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0321 in 152,188 control chromosomes in the GnomAD database, including 112 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 0.032 (112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0321 (4880/152188) while in subpopulation NFE AF= 0.0497 (3378/67984). AF 95% confidence interval is 0.0483. There are 112 homozygotes in gnomad4. There are 2307 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 112 gene

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: 0.0321 AC: 4886 AN: 152070 Hom.: 112 Cov.: 32

Gnomad AFR AF: 0.00908

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0167

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0497

Gnomad OTH AF: 0.0364

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

GnomAD4 genome AF: 0.0321 AC: 4880 AN: 152188 Hom.: 112 Cov.: 32 AF XY: 0.0310 AC XY: 2307 AN XY: 74408

Gnomad4 AFR AF: 0.00905

Gnomad4 AMR AF: 0.0226

Gnomad4 ASJ AF: 0.0479

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0163

Gnomad4 FIN AF: 0.0389

Gnomad4 NFE AF: 0.0497

Gnomad4 OTH AF: 0.0360

Alfa AF: 0.0474 Hom.: 265

Bravo AF: 0.0305

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.3
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11054515; hg19: chr12-12077976;