chr6-22282803-T-C

Position:

• chr6-22282803-T-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 0.229 in 152,086 control chromosomes in the GnomAD database, including 4,511 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 0.23 (4511 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22282803T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000561912.3	n.459-8075T>C		intron_variant		5
CASC15	ENST00000651569.1	n.376-8056T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34802 AN: 151968 Hom.: 4500 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.229 AC: 34865 AN: 152086 Hom.: 4511 Cov.: 32 AF XY: 0.234 AC XY: 17390 AN XY: 74358

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.237

Alfa AF: 0.0630 Hom.: 77

Bravo AF: 0.241

Asia WGS AF: 0.318 AC: 1102 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs849872; hg19: chr6-22283032;