16-52588200-G-A

Position:

• chr16-52588200-G-A

Variant summary

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

The ENST00000650564.1(ENSG00000285800):​n.1237G>A 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 0.198 in 152,034 control chromosomes in the GnomAD database, including 3,072 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 0.20 (3072 hom., cov: 31)
• Consequence: ENSG00000285800 ENST00000650564.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

Genes affected

CASC16 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC16	NR_033920.1	n.604+2736C>T		intron_variant
LOC105371265	XR_933581.3	n.401-242G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC16	ENST00000510238.8	n.614+2736C>T		intron_variant		1
ENSG00000285800	ENST00000650564.1	n.1237G>A		non_coding_transcript_exon_variant	4/4
CASC16	ENST00000563844.1	n.444+2736C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30091 AN: 151916 Hom.: 3066 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.198 AC: 30104 AN: 152034 Hom.: 3072 Cov.: 31 AF XY: 0.192 AC XY: 14235 AN XY: 74302

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.209

Alfa AF: 0.201 Hom.: 878

Bravo AF: 0.203

Asia WGS AF: 0.168 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11640537; hg19: chr16-52622112;