9-24610708-C-G

Variant names:

• chr9-24610708-C-G
• rs1034168

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;