chr9-21078816-C-G

Variant names:

• chr9-21078816-C-G
• rs1424855

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 0.686 in 152,014 control chromosomes in the GnomAD database, including 35,924 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 0.69 (35924 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 6 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 = 0.753 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: 0.686 AC: 104130 AN: 151896 Hom.: 35896 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.686 AC: 104212 AN: 152014 Hom.: 35924 Cov.: 31 AF XY: 0.692 AC XY: 51381 AN XY: 74276

African (AFR) AF: 0.742 AC: 30779 AN: 41458

American (AMR) AF: 0.746 AC: 11379 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3468

East Asian (EAS) AF: 0.773 AC: 4009 AN: 5184

South Asian (SAS) AF: 0.639 AC: 3079 AN: 4822

European-Finnish (FIN) AF: 0.696 AC: 7345 AN: 10556

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43210 AN: 67962

Other (OTH) AF: 0.673 AC: 1421 AN: 2112

Alfa AF: 0.684 Hom.: 4439

Bravo AF: 0.692

Asia WGS AF: 0.694 AC: 2412 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1424855; hg19: chr9-21078815;