rs2866152

Variant names:

• chr4-99329910-G-C
• rs2866152

Your query was ambiguous. Multiple possible variants found:

• chr4-99329910-G-C
• chr4-99329910-G-T

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 0.185 in 152,140 control chromosomes in the GnomAD database, including 2,994 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 0.19 (2994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 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: 0.185 AC: 28193 AN: 152022 Hom.: 2994 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0211

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.185 AC: 28198 AN: 152140 Hom.: 2994 Cov.: 32 AF XY: 0.184 AC XY: 13691 AN XY: 74354

African (AFR) AF: 0.106 AC: 4404 AN: 41538

American (AMR) AF: 0.149 AC: 2276 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3470

East Asian (EAS) AF: 0.0211 AC: 109 AN: 5166

South Asian (SAS) AF: 0.127 AC: 611 AN: 4826

European-Finnish (FIN) AF: 0.297 AC: 3141 AN: 10568

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16467 AN: 67976

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.219 Hom.: 485

Bravo AF: 0.169

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.66
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2866152; hg19: chr4-100251067;