12-94489470-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724960	XR_945224.3	n.214+15859T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;