16-52273164-C-T

Position:

• chr16-52273164-C-T

Variant summary

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

The ENST00000653084.1(CASC22):​n.405C>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 0.263 in 152,046 control chromosomes in the GnomAD database, including 6,283 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 0.26 (6283 hom., cov: 32)
• Consequence: CASC22 ENST00000653084.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

CASC22 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107983961	XR_007065214.1	n.379C>T		non_coding_transcript_exon_variant	2/3
LOC107983961	XR_007065215.1	n.332C>T		non_coding_transcript_exon_variant	2/3
CASC22	NR_135281.1	n.21-6445C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC22	ENST00000653084.1	n.405C>T		non_coding_transcript_exon_variant	2/4
CASC22	ENST00000656784.1	n.427C>T		non_coding_transcript_exon_variant	3/5
CASC22	ENST00000661626.1	n.305C>T		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39960 AN: 151928 Hom.: 6261 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.263 AC: 40025 AN: 152046 Hom.: 6283 Cov.: 32 AF XY: 0.259 AC XY: 19276 AN XY: 74328

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.0953

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.240

Alfa AF: 0.238 Hom.: 542

Bravo AF: 0.276

Asia WGS AF: 0.209 AC: 728 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	2.5
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12325489; hg19: chr16-52307076;