rs12881798

Variant names:

• chr14-94880221-C-A
• rs12881798

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.445 AC: 18425 AN: 41402

American (AMR) AF: 0.307 AC: 4691 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3466

East Asian (EAS) AF: 0.374 AC: 1925 AN: 5148

South Asian (SAS) AF: 0.381 AC: 1835 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2939 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22251 AN: 67934

Other (OTH) AF: 0.338 AC: 713 AN: 2108

Alfa AF: 0.343 Hom.: 27679

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12881798; hg19: chr14-95346558;