rs2864107

Variant names:

• chr19-51565774-G-A
• rs2864107

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 0.41 in 151,954 control chromosomes in the GnomAD database, including 13,412 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 0.41 (13412 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.844
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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: 0.410 AC: 62280 AN: 151836 Hom.: 13406 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.410 AC: 62311 AN: 151954 Hom.: 13412 Cov.: 31 AF XY: 0.408 AC XY: 30261 AN XY: 74258

African (AFR) AF: 0.511 AC: 21153 AN: 41396

American (AMR) AF: 0.494 AC: 7539 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3470

East Asian (EAS) AF: 0.161 AC: 833 AN: 5172

South Asian (SAS) AF: 0.243 AC: 1174 AN: 4826

European-Finnish (FIN) AF: 0.372 AC: 3927 AN: 10564

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24968 AN: 67940

Other (OTH) AF: 0.425 AC: 896 AN: 2110

Alfa AF: 0.413 Hom.: 2343

Bravo AF: 0.428

Asia WGS AF: 0.254 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.63
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs2864107; hg19: chr19-52069027;