12-100467326-G-T

Variant names:

• chr12-100467326-G-T
• rs4764979

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 0.108 in 152,012 control chromosomes in the GnomAD database, including 1,703 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 0.11 (1703 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16453 AN: 151894 Hom.: 1697 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.108 AC: 16485 AN: 152012 Hom.: 1703 Cov.: 32 AF XY: 0.108 AC XY: 7997 AN XY: 74328

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.0591

Gnomad4 ASJ AF: 0.0554

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0302

Gnomad4 NFE AF: 0.0363

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0568 Hom.: 213

Bravo AF: 0.117

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4764979; hg19: chr12-100861104;