rs348484

Variant names:

• chr9-72900409-A-G
• rs348484

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 0.108 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0441 AC: 1831 AN: 41526

American (AMR) AF: 0.0793 AC: 1210 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3468

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5162

South Asian (SAS) AF: 0.0574 AC: 277 AN: 4822

European-Finnish (FIN) AF: 0.107 AC: 1129 AN: 10576

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10858 AN: 67980

Other (OTH) AF: 0.110 AC: 232 AN: 2114

Alfa AF: 0.147 Hom.: 3284

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs348484; hg19: chr9-75515325;