6-22201602-C-T

Position:

• chr6-22201602-C-T

Variant summary

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

The XR_007059494.1(LOC124901275):​n.575C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 152,232 control chromosomes in the GnomAD database, including 579 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 0.080 (579 hom., cov: 32)
• Consequence: LOC124901275 XR_007059494.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

Genes affected

CASC15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901275	XR_007059494.1	n.575C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.1224-3583C>T		intron_variant		1
CASC15	ENST00000561912.3	n.199+54532C>T		intron_variant		5
CASC15	ENST00000567753.2	n.89-12705C>T		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12235 AN: 152114 Hom.: 578 Cov.: 32

Gnomad AFR AF: 0.0475

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0804 AC: 12243 AN: 152232 Hom.: 579 Cov.: 32 AF XY: 0.0842 AC XY: 6266 AN XY: 74410

Gnomad4 AFR AF: 0.0475

Gnomad4 AMR AF: 0.0913

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.0764

Gnomad4 SAS AF: 0.0709

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.0855

Gnomad4 OTH AF: 0.0785

Alfa AF: 0.0817 Hom.: 74

Bravo AF: 0.0716

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7765440; hg19: chr6-22201831;