9-10686696-T-C

Position:

• chr9-10686696-T-C

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 0.0431 in 152,274 control chromosomes in the GnomAD database, including 808 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 0.043 (808 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10686696T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0430 AC: 6543 AN: 152156 Hom.: 803 Cov.: 32

Gnomad AFR AF: 0.00921

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.00574

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00537

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0431 AC: 6565 AN: 152274 Hom.: 808 Cov.: 32 AF XY: 0.0497 AC XY: 3697 AN XY: 74454

Gnomad4 AFR AF: 0.00928

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.00574

Gnomad4 NFE AF: 0.00537

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0238 Hom.: 45

Bravo AF: 0.0581

Asia WGS AF: 0.190 AC: 660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.21
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4623487; hg19: chr9-10686696;