9-21080519-T-C

Variant names:

• chr9-21080519-T-C
• rs10811465

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 0.189 in 152,064 control chromosomes in the GnomAD database, including 3,018 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 0.19 (3018 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28689 AN: 151946 Hom.: 3013 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.189 AC: 28711 AN: 152064 Hom.: 3018 Cov.: 32 AF XY: 0.195 AC XY: 14490 AN XY: 74336

African (AFR) AF: 0.135 AC: 5619 AN: 41512

American (AMR) AF: 0.347 AC: 5302 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3472

East Asian (EAS) AF: 0.278 AC: 1430 AN: 5146

South Asian (SAS) AF: 0.222 AC: 1069 AN: 4816

European-Finnish (FIN) AF: 0.208 AC: 2201 AN: 10574

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11903 AN: 67968

Other (OTH) AF: 0.212 AC: 448 AN: 2114

Alfa AF: 0.180 Hom.: 10434

Bravo AF: 0.199

Asia WGS AF: 0.214 AC: 743 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	0.84
DANN	Benign	0.46
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10811465; hg19: chr9-21080518;