9-104948281-C-T

Variant names:

• chr9-104948281-C-T
• rs2472459

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 0.253 in 152,064 control chromosomes in the GnomAD database, including 5,084 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 0.25 (5084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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: 0.253 AC: 38372 AN: 151946 Hom.: 5082 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.253 AC: 38407 AN: 152064 Hom.: 5084 Cov.: 32 AF XY: 0.256 AC XY: 18998 AN XY: 74330

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.234

Alfa AF: 0.220 Hom.: 6586

Bravo AF: 0.252

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2472459; hg19: chr9-107710562;