14-68863518-T-G

Variant names:

• chr14-68863518-T-G
• rs453964

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 0.629 in 151,852 control chromosomes in the GnomAD database, including 30,771 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 0.63 (30771 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.727 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: 0.629 AC: 95383 AN: 151734 Hom.: 30744 Cov.: 30

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.629 AC: 95441 AN: 151852 Hom.: 30771 Cov.: 30 AF XY: 0.629 AC XY: 46650 AN XY: 74174

African (AFR) AF: 0.494 AC: 20429 AN: 41384

American (AMR) AF: 0.738 AC: 11259 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2219 AN: 3468

East Asian (EAS) AF: 0.524 AC: 2713 AN: 5176

South Asian (SAS) AF: 0.692 AC: 3330 AN: 4812

European-Finnish (FIN) AF: 0.656 AC: 6882 AN: 10494

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46454 AN: 67950

Other (OTH) AF: 0.637 AC: 1345 AN: 2112

Alfa AF: 0.591 Hom.: 3521

Bravo AF: 0.626

Asia WGS AF: 0.661 AC: 2294 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	0.24
DANN	Benign	0.59
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs453964; hg19: chr14-69330235;