9-96805102-C-A

Variant names:

• chr9-96805102-C-A
• rs10124911

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 0.134 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.134 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

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.0676

Gnomad4 ASJ AF: 0.0220

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.0700

Gnomad4 FIN AF: 0.0461

Gnomad4 NFE AF: 0.0151

Gnomad4 OTH AF: 0.0906

Alfa AF: 0.0352 Hom.: 627

Bravo AF: 0.147

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
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: rs10124911; hg19: chr9-99567384;