9-21078816-C-G

Position:

• chr9-21078816-C-G

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21078816C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.673

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424855; hg19: chr9-21078815;