chr12-100467326-G-T

Variant names:

• chr12-100467326-G-T
• rs4764979

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.264 AC: 10943 AN: 41400

American (AMR) AF: 0.0591 AC: 903 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0554 AC: 192 AN: 3468

East Asian (EAS) AF: 0.146 AC: 754 AN: 5176

South Asian (SAS) AF: 0.144 AC: 693 AN: 4802

European-Finnish (FIN) AF: 0.0302 AC: 320 AN: 10588

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2469 AN: 67986

Other (OTH) AF: 0.0790 AC: 167 AN: 2114

Alfa AF: 0.0605 Hom.: 240

Bravo AF: 0.117

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.50
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs4764979; hg19: chr12-100861104;