rs9327886

Variant names:

• chr5-103568046-G-A
• rs9327886

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 0.527 in 152,020 control chromosomes in the GnomAD database, including 21,511 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 0.53 (21511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 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: 0.527 AC: 80085 AN: 151900 Hom.: 21511 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.527 AC: 80109 AN: 152020 Hom.: 21511 Cov.: 32 AF XY: 0.531 AC XY: 39438 AN XY: 74300

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.519

Alfa AF: 0.561 Hom.: 31609

Bravo AF: 0.508

Asia WGS AF: 0.558 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9327886; hg19: chr5-102903747;