5-16286864-A-G

Variant names:

• chr5-16286864-A-G
• rs831657

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 0.777 in 152,038 control chromosomes in the GnomAD database, including 46,399 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 0.78 (46399 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.822 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: 0.777 AC: 118001 AN: 151918 Hom.: 46384 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.777 AC: 118058 AN: 152038 Hom.: 46399 Cov.: 31 AF XY: 0.782 AC XY: 58077 AN XY: 74314

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.765

Alfa AF: 0.810 Hom.: 75816

Bravo AF: 0.760

Asia WGS AF: 0.774 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs831657; hg19: chr5-16286973;