rs12881798

Positions:

• chr14-94880221-C-A

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 0.357 in 151,914 control chromosomes in the GnomAD database, including 9,998 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 0.36 (9998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 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: 0.357 AC: 54265 AN: 151796 Hom.: 9988 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.357 AC: 54301 AN: 151914 Hom.: 9998 Cov.: 32 AF XY: 0.354 AC XY: 26269 AN XY: 74238

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.338

Alfa AF: 0.337 Hom.: 11796

Bravo AF: 0.363

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12881798; hg19: chr14-95346558;