rs9708611

Positions:

• chr16-52578753-G-A

Variant summary

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

The NR_033920.1(CASC16):​n.604+12183C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0422 in 152,254 control chromosomes in the GnomAD database, including 172 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 0.042 (172 hom., cov: 32)
• Consequence: CASC16 NR_033920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

CASC16 (HGNC:48608): (cancer susceptibility 16)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC16	NR_033920.1	n.604+12183C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC16	ENST00000510238.8	n.614+12183C>T		intron_variant, non_coding_transcript_variant		1
CASC16	ENST00000652959.1	n.472-5409C>T		intron_variant, non_coding_transcript_variant
CASC16	ENST00000563844.1	n.445-5409C>T		intron_variant, non_coding_transcript_variant		3
CASC16	ENST00000671536.1	n.621+12183C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0422 AC: 6423 AN: 152136 Hom.: 171 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0615

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0630

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0422 AC: 6423 AN: 152254 Hom.: 172 Cov.: 32 AF XY: 0.0412 AC XY: 3066 AN XY: 74448

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.0343

Gnomad4 ASJ AF: 0.0615

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.0712

Gnomad4 NFE AF: 0.0630

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0530 Hom.: 138

Bravo AF: 0.0368

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.9
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: rs9708611; hg19: chr16-52612665;