rs4465523

Variant names:

• chr14-20445364-G-A
• rs4465523

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 0.344 in 151,998 control chromosomes in the GnomAD database, including 9,222 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 0.34 (9222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52208 AN: 151880 Hom.: 9221 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.344 AC: 52225 AN: 151998 Hom.: 9222 Cov.: 32 AF XY: 0.348 AC XY: 25837 AN XY: 74276

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.369

Alfa AF: 0.359 Hom.: 19890

Bravo AF: 0.325

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4465523; hg19: chr14-20913523;