rs10817408

Variant names:

• chr9-112925455-T-C
• rs10817408

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 0.108 in 152,184 control chromosomes in the GnomAD database, including 1,010 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 0.11 (1010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 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: 0.108 AC: 16459 AN: 152066 Hom.: 1013 Cov.: 32

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.108 AC: 16449 AN: 152184 Hom.: 1010 Cov.: 32 AF XY: 0.109 AC XY: 8124 AN XY: 74396

Gnomad4 AFR AF: 0.0577

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.133

Alfa AF: 0.132 Hom.: 1929

Bravo AF: 0.106

Asia WGS AF: 0.108 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10817408; hg19: chr9-115687735;