9-100689786-G-T

Variant names:

• chr9-100689786-G-T
• rs10123021

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 0.32 in 151,584 control chromosomes in the GnomAD database, including 8,041 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 0.32 (8041 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 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: 0.320 AC: 48474 AN: 151466 Hom.: 8038 Cov.: 29

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.320 AC: 48493 AN: 151584 Hom.: 8041 Cov.: 29 AF XY: 0.316 AC XY: 23429 AN XY: 74058

African (AFR) AF: 0.301 AC: 12426 AN: 41318

American (AMR) AF: 0.244 AC: 3712 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1348 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1539 AN: 5140

South Asian (SAS) AF: 0.220 AC: 1050 AN: 4778

European-Finnish (FIN) AF: 0.355 AC: 3726 AN: 10504

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23736 AN: 67872

Other (OTH) AF: 0.331 AC: 695 AN: 2100

Alfa AF: 0.329 Hom.: 12553

Bravo AF: 0.313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.76
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10123021; hg19: chr9-103452068;