12-101153425-C-T

Variant names:

• chr12-101153425-C-T
• rs223554

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.68 (29650 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.677 AC: 83982 AN: 124030 Hom.: 29629 Cov.: 19

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.700

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.677 AC: 84029 AN: 124096 Hom.: 29650 Cov.: 19 AF XY: 0.675 AC XY: 40584 AN XY: 60116

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.654

Alfa AF: 0.517 Hom.: 1114

Bravo AF: 0.717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223554; hg19: chr12-101547203;