rs2878172

Variant names:

• chr14-54906952-A-G
• rs2878172

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 0.466 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.583 AC: 20750 AN: 35622

American (AMR) AF: 0.394 AC: 5891 AN: 14970

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1067 AN: 3460

East Asian (EAS) AF: 0.181 AC: 934 AN: 5172

South Asian (SAS) AF: 0.388 AC: 1867 AN: 4810

European-Finnish (FIN) AF: 0.614 AC: 6495 AN: 10570

Middle Eastern (MID) AF: 0.208 AC: 60 AN: 288

European-Non Finnish (NFE) AF: 0.434 AC: 29472 AN: 67886

Other (OTH) AF: 0.415 AC: 850 AN: 2048

Alfa AF: 0.448 Hom.: 8629

Bravo AF: 0.429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.39
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2878172; hg19: chr14-55373670;