chr9-96805102-C-A

Variant names:

• chr9-96805102-C-A
• rs10124911

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 0.134 in 151,528 control chromosomes in the GnomAD database, including 3,326 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 0.13 (3326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20278 AN: 151410 Hom.: 3292 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0220

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0706

Gnomad FIN AF: 0.0461

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0151

Gnomad OTH AF: 0.0920

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

GnomAD4 genome AF: 0.134 AC: 20354 AN: 151528 Hom.: 3326 Cov.: 32 AF XY: 0.135 AC XY: 10000 AN XY: 74064

African (AFR) AF: 0.386 AC: 15945 AN: 41318

American (AMR) AF: 0.0676 AC: 1030 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0220 AC: 76 AN: 3462

East Asian (EAS) AF: 0.239 AC: 1235 AN: 5162

South Asian (SAS) AF: 0.0700 AC: 337 AN: 4814

European-Finnish (FIN) AF: 0.0461 AC: 483 AN: 10474

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0151 AC: 1025 AN: 67764

Other (OTH) AF: 0.0906 AC: 190 AN: 2098

Alfa AF: 0.0528 Hom.: 3384

Bravo AF: 0.147

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.34
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10124911; hg19: chr9-99567384;