12-126508343-G-C

Position:

• chr12-126508343-G-C

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 0.0628 in 149,964 control chromosomes in the GnomAD database, including 319 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 0.063 (319 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0834 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: 0.0627 AC: 9404 AN: 149892 Hom.: 320 Cov.: 31

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.0266

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.0546

Gnomad OTH AF: 0.0638

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

GnomAD4 genome AF: 0.0628 AC: 9414 AN: 149964 Hom.: 319 Cov.: 31 AF XY: 0.0626 AC XY: 4579 AN XY: 73128

Gnomad4 AFR AF: 0.0858

Gnomad4 AMR AF: 0.0557

Gnomad4 ASJ AF: 0.0858

Gnomad4 EAS AF: 0.0267

Gnomad4 SAS AF: 0.0524

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.0546

Gnomad4 OTH AF: 0.0637

Alfa AF: 0.0142 Hom.: 4

Bravo AF: 0.0651

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492049; hg19: chr12-126992889;