14-20479109-T-G

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 0.454 in 152,044 control chromosomes in the GnomAD database, including 16,299 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 0.45 (16299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 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: 0.453 AC: 68884 AN: 151926 Hom.: 16280 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.454 AC: 68962 AN: 152044 Hom.: 16299 Cov.: 32 AF XY: 0.456 AC XY: 33927 AN XY: 74324

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.448

Alfa AF: 0.386 Hom.: 13434

Bravo AF: 0.453

Asia WGS AF: 0.493 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.2
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1760931; hg19: chr14-20947268;