rs12894364

Positions:

• chr14-37588860-C-T

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 0.078 in 152,232 control chromosomes in the GnomAD database, including 639 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 0.078 (639 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.936

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 11858 AN: 152114 Hom.: 629 Cov.: 33

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0780 AC: 11879 AN: 152232 Hom.: 639 Cov.: 33 AF XY: 0.0837 AC XY: 6227 AN XY: 74438

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.0916

Gnomad4 OTH AF: 0.0737

Alfa AF: 0.0871 Hom.: 677

Bravo AF: 0.0642

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12894364; hg19: chr14-38058065;