chr12-94489470-T-C

Variant names:

• chr12-94489470-T-C
• rs2128894
• XR_945224.3:n.214+15859T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_945224.3(LOC102724960):​n.214+15859T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,078 control chromosomes in the GnomAD database, including 33,489 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 0.66 (33489 hom., cov: 33)
• Consequence: LOC102724960 XR_945224.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 2 publications found

Genes affected

LOC102724960 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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: 0.661 AC: 100507 AN: 151960 Hom.: 33463 Cov.: 33

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.622

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.661 AC: 100580 AN: 152078 Hom.: 33489 Cov.: 33 AF XY: 0.658 AC XY: 48923 AN XY: 74318

African (AFR) AF: 0.696 AC: 28870 AN: 41478

American (AMR) AF: 0.546 AC: 8340 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2130 AN: 3468

East Asian (EAS) AF: 0.720 AC: 3723 AN: 5172

South Asian (SAS) AF: 0.674 AC: 3254 AN: 4826

European-Finnish (FIN) AF: 0.677 AC: 7147 AN: 10560

Middle Eastern (MID) AF: 0.610 AC: 177 AN: 290

European-Non Finnish (NFE) AF: 0.661 AC: 44967 AN: 67984

Other (OTH) AF: 0.645 AC: 1364 AN: 2114

Alfa AF: 0.646 Hom.: 41312

Bravo AF: 0.649

Asia WGS AF: 0.699 AC: 2431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.9
DANN	Benign	0.74
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2128894; hg19: chr12-94883246;