chr9-24610708-C-G

Position:

• chr9-24610708-C-G

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 0.0913 in 151,934 control chromosomes in the GnomAD database, including 800 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 0.091 (800 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24610708C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0912 AC: 13853 AN: 151816 Hom.: 797 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.0913 AC: 13876 AN: 151934 Hom.: 800 Cov.: 32 AF XY: 0.0903 AC XY: 6708 AN XY: 74248

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0729

Gnomad4 EAS AF: 0.0341

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0905

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.0996

Alfa AF: 0.0282 Hom.: 25

Bravo AF: 0.0878

Asia WGS AF: 0.115 AC: 400 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1034168; hg19: chr9-24610706;