rs11640537

Variant names:

• chr16-52588200-G-A
• rs11640537
• ENST00000510238.9:n.621+2736C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ENSG00000285800 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650564.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	NR_033920.1		n.604+2736C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000510238.9	TSL:1	n.621+2736C>T		intron	N/A
	ENSG00000285800	ENST00000650564.1		n.1237G>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000285800	ENST00000826653.1		n.642G>A		non_coding_transcript_exon	Exon 3 of 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

African (AFR) AF: 0.206 AC: 8545 AN: 41470

American (AMR) AF: 0.202 AC: 3092 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3468

East Asian (EAS) AF: 0.159 AC: 814 AN: 5132

South Asian (SAS) AF: 0.192 AC: 924 AN: 4808

European-Finnish (FIN) AF: 0.129 AC: 1366 AN: 10576

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13941 AN: 67990

Other (OTH) AF: 0.209 AC: 442 AN: 2110

Alfa AF: 0.200 Hom.: 1530

Bravo AF: 0.203

Asia WGS AF: 0.168 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs11640537; hg19: chr16-52622112;