rs2863274

Variant names:

• chr15-99554520-T-C
• rs2863274

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 0.25 in 152,202 control chromosomes in the GnomAD database, including 5,518 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 0.25 (5518 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 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: 0.250 AC: 38082 AN: 152084 Hom.: 5516 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.250 AC: 38097 AN: 152202 Hom.: 5518 Cov.: 33 AF XY: 0.257 AC XY: 19101 AN XY: 74408

African (AFR) AF: 0.101 AC: 4188 AN: 41562

American (AMR) AF: 0.250 AC: 3822 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1358 AN: 5180

South Asian (SAS) AF: 0.346 AC: 1672 AN: 4826

European-Finnish (FIN) AF: 0.395 AC: 4182 AN: 10576

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20742 AN: 67980

Other (OTH) AF: 0.286 AC: 603 AN: 2112

Alfa AF: 0.288 Hom.: 25612

Bravo AF: 0.233

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.47
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2863274; hg19: chr15-100094725;