14-88906407-A-G

Variant names:

• chr14-88906407-A-G
• rs17124955

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 0.0846 in 152,142 control chromosomes in the GnomAD database, including 1,320 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 0.085 (1320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12826 AN: 152022 Hom.: 1309 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0663

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.0328

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00734

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0846 AC: 12875 AN: 152142 Hom.: 1320 Cov.: 32 AF XY: 0.0846 AC XY: 6293 AN XY: 74390

African (AFR) AF: 0.237 AC: 9839 AN: 41442

American (AMR) AF: 0.0666 AC: 1018 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3470

East Asian (EAS) AF: 0.162 AC: 834 AN: 5164

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4822

European-Finnish (FIN) AF: 0.0328 AC: 348 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00734 AC: 499 AN: 68018

Other (OTH) AF: 0.0662 AC: 140 AN: 2114

Alfa AF: 0.0374 Hom.: 1132

Bravo AF: 0.0948

Asia WGS AF: 0.0930 AC: 324 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	4.3
DANN	Benign	0.43
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs17124955; hg19: chr14-89372751;