12-101153425-C-T

Variant names:

• chr12-101153425-C-T
• rs223554

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.832 AC: 21948 AN: 26372

American (AMR) AF: 0.605 AC: 7688 AN: 12700

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2191 AN: 3178

East Asian (EAS) AF: 0.811 AC: 3895 AN: 4802

South Asian (SAS) AF: 0.681 AC: 2538 AN: 3726

European-Finnish (FIN) AF: 0.631 AC: 5935 AN: 9410

Middle Eastern (MID) AF: 0.690 AC: 178 AN: 258

European-Non Finnish (NFE) AF: 0.623 AC: 38074 AN: 61086

Other (OTH) AF: 0.654 AC: 1114 AN: 1704

Alfa AF: 0.517 Hom.: 1114

Bravo AF: 0.717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs223554; hg19: chr12-101547203;