rs9325117

Variant names:

• chr5-148795484-A-G
• rs9325117

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.142 in 152,196 control chromosomes in the GnomAD database, including 4,379 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 0.14 (4379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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: 0.142 AC: 21608 AN: 152078 Hom.: 4357 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.142 AC: 21681 AN: 152196 Hom.: 4379 Cov.: 32 AF XY: 0.141 AC XY: 10471 AN XY: 74446

African (AFR) AF: 0.447 AC: 18548 AN: 41466

American (AMR) AF: 0.0516 AC: 790 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00577 AC: 20 AN: 3468

East Asian (EAS) AF: 0.110 AC: 572 AN: 5182

South Asian (SAS) AF: 0.0516 AC: 249 AN: 4824

European-Finnish (FIN) AF: 0.0463 AC: 491 AN: 10616

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0115 AC: 784 AN: 68018

Other (OTH) AF: 0.102 AC: 216 AN: 2116

Alfa AF: 0.0610 Hom.: 3895

Bravo AF: 0.158

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.18
DANN	Benign	0.56
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs9325117; hg19: chr5-148175047;