chr14-94880221-C-A

Variant names:

• chr14-94880221-C-A
• rs12881798

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;