rs2919872

Variant names:

• chr2-88129052-C-T
• rs2919872

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 0.401 in 152,048 control chromosomes in the GnomAD database, including 13,228 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 0.40 (13228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 16 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 (NFE) allele frequency at 95% confidence interval = 0.454 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: 0.401 AC: 60960 AN: 151930 Hom.: 13226 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.401 AC: 60975 AN: 152048 Hom.: 13228 Cov.: 32 AF XY: 0.403 AC XY: 29980 AN XY: 74318

African (AFR) AF: 0.271 AC: 11245 AN: 41492

American (AMR) AF: 0.448 AC: 6846 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5162

South Asian (SAS) AF: 0.222 AC: 1073 AN: 4824

European-Finnish (FIN) AF: 0.639 AC: 6752 AN: 10574

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31154 AN: 67948

Other (OTH) AF: 0.406 AC: 855 AN: 2106

Alfa AF: 0.427 Hom.: 38688

Bravo AF: 0.383

Asia WGS AF: 0.225 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2919872; hg19: chr2-88428571;