rs9325124

Positions:

• chr5-148869255-G-A
• chr5-148869255-G-C
• chr5-148869255-G-T

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 0.494 in 151,392 control chromosomes in the GnomAD database, including 19,303 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 0.49 (19303 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

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 (EAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74789 AN: 151272 Hom.: 19293 Cov.: 30

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.494 AC: 74835 AN: 151392 Hom.: 19303 Cov.: 30 AF XY: 0.494 AC XY: 36531 AN XY: 73896

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.463

Alfa AF: 0.432 Hom.: 23115

Bravo AF: 0.513

Asia WGS AF: 0.463 AC: 1608 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9325124; hg19: chr5-148248818;