rs9313999

Variant names:

• chr5-164084985-A-G
• rs9313999

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 0.617 in 151,724 control chromosomes in the GnomAD database, including 29,297 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 0.62 (29297 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.616 AC: 93450 AN: 151606 Hom.: 29264 Cov.: 31

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.617 AC: 93538 AN: 151724 Hom.: 29297 Cov.: 31 AF XY: 0.613 AC XY: 45384 AN XY: 74090

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.610

Alfa AF: 0.582 Hom.: 44563

Bravo AF: 0.623

Asia WGS AF: 0.505 AC: 1750 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9313999; hg19: chr5-163511991;