chr6-21785940-C-T

Position:

• chr6-21785940-C-T

Variant summary

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

The ENST00000606336.5(CASC15):​n.920+2232C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,878 control chromosomes in the GnomAD database, including 2,909 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 0.19 (2909 hom., cov: 32)
• Consequence: CASC15 ENST00000606336.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

Genes affected

CASC15 (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 = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC15	NR_015410.2	n.563+2232C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000606336.5	n.920+2232C>T		intron_variant		1
CASC15	ENST00000606851.5	n.532+2232C>T		intron_variant		2
CASC15	ENST00000607048.5	n.158+2232C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28178 AN: 151762 Hom.: 2906 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.186 AC: 28202 AN: 151878 Hom.: 2909 Cov.: 32 AF XY: 0.179 AC XY: 13264 AN XY: 74208

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0644

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.173

Alfa AF: 0.178 Hom.: 5277

Bravo AF: 0.189

Asia WGS AF: 0.0440 AC: 155 AN: 3478

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	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9466182; hg19: chr6-21786171;