rs8020463

Variant names:

• chr14-23035574-A-G
• rs8020463

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 0.538 in 152,070 control chromosomes in the GnomAD database, including 25,804 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 0.54 (25804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.537 AC: 81662 AN: 151954 Hom.: 25741 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.538 AC: 81766 AN: 152070 Hom.: 25804 Cov.: 32 AF XY: 0.530 AC XY: 39421 AN XY: 74326

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.527

Alfa AF: 0.468 Hom.: 4933

Bravo AF: 0.547

Asia WGS AF: 0.388 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8020463; hg19: chr14-23504783;