rs348484

Variant names:

• chr9-72900409-A-G
• rs348484

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 0.108 in 152,108 control chromosomes in the GnomAD database, including 1,103 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 0.11 (1103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 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: 0.108 AC: 16463 AN: 151990 Hom.: 1103 Cov.: 32

Gnomad AFR AF: 0.0441

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0796

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0576

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.108 AC: 16458 AN: 152108 Hom.: 1103 Cov.: 32 AF XY: 0.104 AC XY: 7716 AN XY: 74358

Gnomad4 AFR AF: 0.0441

Gnomad4 AMR AF: 0.0793

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.0574

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.110

Alfa AF: 0.153 Hom.: 2522

Bravo AF: 0.105

Asia WGS AF: 0.0500 AC: 173 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs348484; hg19: chr9-75515325;