chr9-21149392-A-G

Variant names:

• chr9-21149392-A-G
• rs10081742

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 0.146 in 152,200 control chromosomes in the GnomAD database, including 1,778 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 0.15 (1778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.189 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: 0.146 AC: 22222 AN: 152082 Hom.: 1779 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0919

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0806

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.146 AC: 22229 AN: 152200 Hom.: 1778 Cov.: 32 AF XY: 0.146 AC XY: 10892 AN XY: 74422

African (AFR) AF: 0.171 AC: 7109 AN: 41522

American (AMR) AF: 0.187 AC: 2861 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3468

East Asian (EAS) AF: 0.0915 AC: 473 AN: 5170

South Asian (SAS) AF: 0.200 AC: 964 AN: 4822

European-Finnish (FIN) AF: 0.0806 AC: 856 AN: 10614

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.133 AC: 9060 AN: 67998

Other (OTH) AF: 0.140 AC: 297 AN: 2114

Alfa AF: 0.133 Hom.: 166

Bravo AF: 0.153

Asia WGS AF: 0.145 AC: 504 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	3.6
DANN	Benign	0.71
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10081742; hg19: chr9-21149391;