14-53984584-A-G

Variant names:

• chr14-53984584-A-G
• rs11157994

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 0.79 in 152,064 control chromosomes in the GnomAD database, including 50,161 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 0.79 (50161 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 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: 0.791 AC: 120151 AN: 151946 Hom.: 50150 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.790 AC: 120199 AN: 152064 Hom.: 50161 Cov.: 31 AF XY: 0.792 AC XY: 58904 AN XY: 74338

African (AFR) AF: 0.515 AC: 21300 AN: 41396

American (AMR) AF: 0.776 AC: 11848 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3021 AN: 3472

East Asian (EAS) AF: 0.592 AC: 3057 AN: 5164

South Asian (SAS) AF: 0.867 AC: 4178 AN: 4818

European-Finnish (FIN) AF: 0.974 AC: 10341 AN: 10616

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63646 AN: 68012

Other (OTH) AF: 0.795 AC: 1675 AN: 2106

Alfa AF: 0.878 Hom.: 188573

Bravo AF: 0.757

Asia WGS AF: 0.756 AC: 2629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.14
DANN	Benign	0.80
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs11157994; hg19: chr14-54451302;