9-72897384-T-G

Variant names:

• chr9-72897384-T-G
• rs348479

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 0.229 in 151,948 control chromosomes in the GnomAD database, including 4,416 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 0.23 (4416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 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: 0.229 AC: 34721 AN: 151830 Hom.: 4399 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.229 AC: 34774 AN: 151948 Hom.: 4416 Cov.: 31 AF XY: 0.220 AC XY: 16328 AN XY: 74266

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.0360

Gnomad4 SAS AF: 0.0807

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.216

Alfa AF: 0.221 Hom.: 5248

Bravo AF: 0.239

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs348479; hg19: chr9-75512300;