rs12883544

Positions:

• chr14-97026174-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 0.35 in 151,972 control chromosomes in the GnomAD database, including 9,760 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 0.35 (9760 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.927

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 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: 0.350 AC: 53124 AN: 151854 Hom.: 9765 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.350 AC: 53124 AN: 151972 Hom.: 9760 Cov.: 31 AF XY: 0.350 AC XY: 25992 AN XY: 74310

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.0808

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.327

Alfa AF: 0.381 Hom.: 1369

Bravo AF: 0.341

Asia WGS AF: 0.249 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12883544; hg19: chr14-97492511;