rs9327881

Variant names:

• chr5-103389394-G-A
• rs9327881

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 0.123 in 152,046 control chromosomes in the GnomAD database, including 1,447 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 0.12 (1447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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: 0.123 AC: 18658 AN: 151928 Hom.: 1445 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0587

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.123 AC: 18676 AN: 152046 Hom.: 1447 Cov.: 32 AF XY: 0.122 AC XY: 9077 AN XY: 74344

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.0727

Gnomad4 ASJ AF: 0.0779

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0589

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0860

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0919 Hom.: 700

Bravo AF: 0.128

Asia WGS AF: 0.0860 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.026
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9327881; hg19: chr5-102725095;