9-107921171-A-G

Variant names:

• chr9-107921171-A-G
• rs12379423

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 0.0639 in 152,260 control chromosomes in the GnomAD database, including 412 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 0.064 (412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.136 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: 0.0640 AC: 9731 AN: 152142 Hom.: 411 Cov.: 32

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0946

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0689

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

GnomAD4 genome AF: 0.0639 AC: 9737 AN: 152260 Hom.: 412 Cov.: 32 AF XY: 0.0665 AC XY: 4947 AN XY: 74442

African (AFR) AF: 0.0158 AC: 658 AN: 41578

American (AMR) AF: 0.122 AC: 1867 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3470

East Asian (EAS) AF: 0.145 AC: 750 AN: 5176

South Asian (SAS) AF: 0.0497 AC: 240 AN: 4826

European-Finnish (FIN) AF: 0.0946 AC: 1003 AN: 10600

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0708 AC: 4814 AN: 68014

Other (OTH) AF: 0.0705 AC: 149 AN: 2112

Alfa AF: 0.0287 Hom.: 20

Bravo AF: 0.0650

Asia WGS AF: 0.0980 AC: 342 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	0.80
DANN	Benign	0.77
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs12379423; hg19: chr9-110683452;