chr12-90396323-C-T

Variant names:

• chr12-90396323-C-T
• rs704106

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 0.741 in 152,176 control chromosomes in the GnomAD database, including 43,137 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 0.74 (43137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 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: 0.741 AC: 112672 AN: 152058 Hom.: 43079 Cov.: 32

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.741 AC: 112789 AN: 152176 Hom.: 43137 Cov.: 32 AF XY: 0.738 AC XY: 54914 AN XY: 74360

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.722

Alfa AF: 0.664 Hom.: 68217

Bravo AF: 0.756

Asia WGS AF: 0.804 AC: 2793 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	0.36
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs704106; hg19: chr12-90790100;