9-24901569-T-C

Position:

• chr9-24901569-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.261 in 152,030 control chromosomes in the GnomAD database, including 5,864 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 0.26 (5864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39629 AN: 151912 Hom.: 5879 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.261 AC: 39622 AN: 152030 Hom.: 5864 Cov.: 32 AF XY: 0.262 AC XY: 19493 AN XY: 74316

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.306

Alfa AF: 0.290 Hom.: 3237

Bravo AF: 0.260

Asia WGS AF: 0.320 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	16
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1932420; hg19: chr9-24901567;