rs2116714

Variant names:

• chr5-148811835-G-A
• rs2116714

Your query was ambiguous. Multiple possible variants found:

• chr5-148811835-G-A
• chr5-148811835-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 0.155 in 151,964 control chromosomes in the GnomAD database, including 4,881 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 0.16 (4881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23495 AN: 151846 Hom.: 4865 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0788

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.00587

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00852

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.155 AC: 23559 AN: 151964 Hom.: 4881 Cov.: 32 AF XY: 0.155 AC XY: 11497 AN XY: 74290

African (AFR) AF: 0.468 AC: 19355 AN: 41390

American (AMR) AF: 0.0785 AC: 1198 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1167 AN: 5170

South Asian (SAS) AF: 0.174 AC: 838 AN: 4806

European-Finnish (FIN) AF: 0.00587 AC: 62 AN: 10566

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00852 AC: 579 AN: 67974

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.0610 Hom.: 3964

Bravo AF: 0.173

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.31
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2116714; hg19: chr5-148191398;