chr6-22139775-A-G

Position:

• chr6-22139775-A-G

Variant summary

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

The ENST00000444265.6(CASC15):​n.1061+28855A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,118 control chromosomes in the GnomAD database, including 30,806 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 0.62 (30806 hom., cov: 32)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

Genes affected

CASC15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC15	NR_015410.2	n.1422+28855A>G		intron_variant
NBAT1	NR_034143.1	n.228-3106T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.1061+28855A>G		intron_variant		1
NBAT1	ENST00000566912.2	n.228-3106T>C		intron_variant		2
CASC15	ENST00000606851.5	n.1391+28855A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93666 AN: 152000 Hom.: 30753 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.616 AC: 93773 AN: 152118 Hom.: 30806 Cov.: 32 AF XY: 0.621 AC XY: 46154 AN XY: 74360

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.572

Alfa AF: 0.500 Hom.: 44492

Bravo AF: 0.627

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.011
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6939340; hg19: chr6-22140004;