chr8-22011513-G-C

Position:

• chr8-22011513-G-C

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 0.575 in 151,768 control chromosomes in the GnomAD database, including 25,640 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 0.57 (25640 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22011513G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87158 AN: 151650 Hom.: 25600 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.575 AC: 87257 AN: 151768 Hom.: 25640 Cov.: 31 AF XY: 0.568 AC XY: 42125 AN XY: 74146

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.568

Alfa AF: 0.554 Hom.: 2785

Bravo AF: 0.578

Asia WGS AF: 0.532 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7013323; hg19: chr8-21869024;