chr12-33718488-G-A

Position:

• chr12-33718488-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 0.277 in 152,020 control chromosomes in the GnomAD database, including 7,127 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 0.28 (7127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42028 AN: 151902 Hom.: 7126 Cov.: 32

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.277 AC: 42035 AN: 152020 Hom.: 7127 Cov.: 32 AF XY: 0.278 AC XY: 20643 AN XY: 74274

Gnomad4 AFR AF: 0.0901

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.0648

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.281

Alfa AF: 0.300 Hom.: 1004

Bravo AF: 0.266

Asia WGS AF: 0.147 AC: 512 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	0.86
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3862406; hg19: chr12-33871423;