chr6-22038297-A-G

Position:

• chr6-22038297-A-G

Variant summary

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

The ENST00000444265.6(CASC15):​n.521+17755A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,132 control chromosomes in the GnomAD database, including 3,903 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 (3903 hom., cov: 32)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

Genes affected

CASC15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC15	NR_015410.2	n.1103+17755A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.521+17755A>G		intron_variant		1
CASC15	ENST00000606851.5	n.1072+17755A>G		intron_variant		2
CASC15	ENST00000607048.5	n.698+17755A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28164 AN: 152014 Hom.: 3898 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0881

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.185 AC: 28201 AN: 152132 Hom.: 3903 Cov.: 32 AF XY: 0.181 AC XY: 13467 AN XY: 74392

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0486

Gnomad4 FIN AF: 0.0881

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.175

Alfa AF: 0.121 Hom.: 2033

Bravo AF: 0.201

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1207774; hg19: chr6-22038526;