chr9-112925455-T-C

Variant names:

• chr9-112925455-T-C
• rs10817408

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0577 AC: 2395 AN: 41520

American (AMR) AF: 0.114 AC: 1748 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3472

East Asian (EAS) AF: 0.106 AC: 550 AN: 5178

South Asian (SAS) AF: 0.126 AC: 607 AN: 4826

European-Finnish (FIN) AF: 0.114 AC: 1206 AN: 10586

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9045 AN: 68004

Other (OTH) AF: 0.133 AC: 281 AN: 2110

Alfa AF: 0.124 Hom.: 2463

Bravo AF: 0.106

Asia WGS AF: 0.108 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10817408; hg19: chr9-115687735;