6-22285783-A-G

Position:

• chr6-22285783-A-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 0.556 in 151,704 control chromosomes in the GnomAD database, including 25,385 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 0.56 (25385 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22285783A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000561912.3	n.459-5095A>G		intron_variant		5
CASC15	ENST00000651569.1	n.376-5076A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84355 AN: 151584 Hom.: 25377 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.556 AC: 84403 AN: 151704 Hom.: 25385 Cov.: 31 AF XY: 0.565 AC XY: 41869 AN XY: 74102

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.600

Alfa AF: 0.624 Hom.: 39328

Bravo AF: 0.552

Asia WGS AF: 0.771 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1205961; hg19: chr6-22286012;