rs10219670

Variant names:

• chr12-105714941-C-A
• rs10219670
• ENST00000547465.1:n.83+8085C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000547465.1(CASC18):​n.83+8085C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 152,012 control chromosomes in the GnomAD database, including 28,052 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 0.60 (28052 hom., cov: 32)
• Consequence: CASC18 ENST00000547465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 4 publications found

Genes affected

CASC18 (HGNC:49463): (cancer susceptibility 18)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547465.1. 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
	CASC18	NR_110108.1		n.54+10685C>A		intron	N/A
	CASC18	NR_110109.1		n.55-221C>A		intron	N/A
	CASC18	NR_110110.1		n.83+8085C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC18	ENST00000547465.1	TSL:1	n.83+8085C>A		intron	N/A
	CASC18	ENST00000548557.1	TSL:1	n.54+10685C>A		intron	N/A
	CASC18	ENST00000656319.1		n.144+9543C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91700 AN: 151894 Hom.: 28011 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.604 AC: 91799 AN: 152012 Hom.: 28052 Cov.: 32 AF XY: 0.597 AC XY: 44314 AN XY: 74286

African (AFR) AF: 0.676 AC: 28049 AN: 41468

American (AMR) AF: 0.663 AC: 10130 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2534 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2818 AN: 5160

South Asian (SAS) AF: 0.386 AC: 1856 AN: 4814

European-Finnish (FIN) AF: 0.481 AC: 5080 AN: 10570

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39208 AN: 67936

Other (OTH) AF: 0.623 AC: 1315 AN: 2112

Alfa AF: 0.618 Hom.: 16655

Bravo AF: 0.627

Asia WGS AF: 0.494 AC: 1721 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.62
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10219670;

hg19: chr12-106108719;