rs878815

Variant names:

• chr14-66025389-G-A
• rs878815

Your query was ambiguous. Multiple possible variants found:

• chr14-66025389-G-A
• chr14-66025389-G-C
• chr14-66025389-G-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 0.515 in 152,142 control chromosomes in the GnomAD database, including 22,684 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 0.52 (22684 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.515 AC: 78270 AN: 152024 Hom.: 22633 Cov.: 33

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.515 AC: 78382 AN: 152142 Hom.: 22684 Cov.: 33 AF XY: 0.515 AC XY: 38322 AN XY: 74372

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.470

Alfa AF: 0.400 Hom.: 7623

Bravo AF: 0.525

Asia WGS AF: 0.439 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs878815; hg19: chr14-66492107;