rs2878172

Variant names:

• chr14-54906952-A-G
• rs2878172

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 0.466 in 145,734 control chromosomes in the GnomAD database, including 15,859 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 0.47 (15859 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 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: 0.466 AC: 67891 AN: 145624 Hom.: 15835 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.216

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.466 AC: 67983 AN: 145734 Hom.: 15859 Cov.: 31 AF XY: 0.471 AC XY: 33644 AN XY: 71376

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.415

Alfa AF: 0.440 Hom.: 1414

Bravo AF: 0.429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2878172; hg19: chr14-55373670;