chr6-22045415-A-G

Position:

• chr6-22045415-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000444265.6(CASC15):​n.522-11131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,010 control chromosomes in the GnomAD database, including 2,663 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 0.18 (2663 hom., cov: 31)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.915

Genes affected

CASC15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC15	NR_015410.2	n.1104-11131A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.522-11131A>G		intron_variant		1
CASC15	ENST00000606851.5	n.1073-11131A>G		intron_variant		2
CASC15	ENST00000607048.5	n.699-11131A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27994 AN: 151892 Hom.: 2653 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.184 AC: 28031 AN: 152010 Hom.: 2663 Cov.: 31 AF XY: 0.190 AC XY: 14106 AN XY: 74276

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.171

Alfa AF: 0.180 Hom.: 3608

Bravo AF: 0.177

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	11
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs993600; hg19: chr6-22045644;