chr6-22540536-C-T

Position:

• chr6-22540536-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652081.1(CASC15):​n.146-33583C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,938 control chromosomes in the GnomAD database, including 17,278 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 0.47 (17278 hom., cov: 33)
• Consequence: CASC15 ENST00000652081.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

Genes affected

CASC15 (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 (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374971	XR_001744025.1	n.488+22766C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000652081.1	n.146-33583C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71386 AN: 151820 Hom.: 17261 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.470 AC: 71447 AN: 151938 Hom.: 17278 Cov.: 33 AF XY: 0.462 AC XY: 34328 AN XY: 74246

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.454

Alfa AF: 0.477 Hom.: 16222

Bravo AF: 0.464

Asia WGS AF: 0.252 AC: 873 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295552; hg19: chr6-22540765;