rs451066

chr14-68758968-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.167 in 152,016 control chromosomes in the GnomAD database, including 2,593 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 0.17 (2593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25307 AN: 151898 Hom.: 2595 Cov.: 32

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.167 AC: 25316 AN: 152016 Hom.: 2593 Cov.: 32 AF XY: 0.164 AC XY: 12225 AN XY: 74324

Gnomad4 AFR AF: 0.0682

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.169

Alfa AF: 0.183 Hom.: 368

Bravo AF: 0.180

Asia WGS AF: 0.149 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.7
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs451066; hg19: chr14-69225685;